Proteopedia - User contributions [en]

https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Stephanie+Maung Proteopedia - User contributions [en] 2026-09-23T11:54:14Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388220 User:Stephanie Maung/Sandbox 2012-05-04T20:28:07Z

<p>Stephanie Maung: </p> <hr /> <div>Outer Surface Protein B (OspB) has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = Background =<br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB. The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. <ref name="Versatile"/>. <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab <ref>PMID: 9038292 </ref>.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1P4P' size='250' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops 1, 2, and 3</scene>. When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>. In <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>H-6831 free</scene> and <scene name='User:Stephanie_Maung/Sandbox/1rjl_chainc/1'>H-6831 bound</scene> forms of OspB, some changes result from proteolysis near the N terminus <ref name="Versatile"/>. Residues 157 - 201 on OspB contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene>, shown in plum.<br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain <ref name="Versatile"/><br /> <br /> <br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102 <ref> PMID:12475199</ref>.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis. A concerted proton transfer, similar to a “proton wire”, is one plausible mechanism that would allow argenine to function in the catalytic triad of a protease <ref name=”Structural”/>. <br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> It was recently discovered that all antibodies contained Fab portions that catalyze a reaction between singlet oxygen and water, which yields hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and is the product of a possible ancient mechanism used protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement <ref name=”Structural”/>.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388219 User:Stephanie Maung/Sandbox 2012-05-04T20:24:09Z

<p>Stephanie Maung: </p> <hr /> <div>Outer Surface Protein B (OspB) has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = Background =<br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>. The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class.<br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab <ref>PMID: 9038292 </ref>.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1P4P' size='250' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops 1, 2, and 3</scene>. When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>. In <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>H-6831 free</scene> and <scene name='User:Stephanie_Maung/Sandbox/1rjl_chainc/1'>H-6831 bound</scene> forms of OspB, some changes result from proteolysis near the N terminus <ref name="Versatile"/>. Residues 157 - 201 on OspB contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene>, shown in plum.<br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain <ref name="Versatile"/><br /> <br /> <br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis. A concerted proton transfer, similar to a “proton wire”, is one plausible mechanism that would allow argenine to function in the catalytic triad of a protease. <br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> It was recently discovered that all antibodies contained Fab portions that catalyze a reaction between singlet oxygen and water, which yields hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and is the product of a possible ancient mechanism used protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388206 User:Stephanie Maung/Sandbox 2012-05-04T20:16:10Z

<p>Stephanie Maung: </p> <hr /> <div>Outer Surface Protein B (OspB) has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = Background =<br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>. The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class.<br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab <ref>PMID: 9038292 </ref>.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1P4P' size='250' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops 1, 2, and 3</scene>. When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>. In <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>H-6831 free</scene> and <scene name='User:Stephanie_Maung/Sandbox/1rjl_chainc/1'>H-6831 bound</scene> forms of OspB, some changes result from proteolysis near the N terminus <ref name="Versatile"/>. Residues 157 - 201 on OspB contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene>, shown in plum.<br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain <ref name="Versatile"/><br /> <br /> <br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388199 User:Stephanie Maung/Sandbox 2012-05-04T20:09:03Z

<p>Stephanie Maung: </p> <hr /> <div>Outer Surface Protein B (OspB) has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = Background =<br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>. The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class.<br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab <ref>PMID: 9038292 </ref>.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1P4P' size='250' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops 1, 2, and 3</scene>. When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>. In <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>H-6831-free</scene> and <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>H-6831 bound</scene> (residues 157-201) forms of OspB, some changes result from proteolysis near the N terminus <ref name="Versatile"/>.<br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain <ref name="Versatile"/><br /> <br /> <br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388198 User:Stephanie Maung/Sandbox 2012-05-04T20:08:29Z

<p>Stephanie Maung: </p> <hr /> <div>Outer Surface Protein B (OspB) has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = Background =<br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>. The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class.<br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab <ref>PMID: 9038292 </ref>.<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1P4P' size='250' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops 1, 2, and 3</scene>. When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>. In <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>H-6831-free</scene> and <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>H-6831 bound</scene> (residues 157-201) forms of OspB, some changes result from proteolysis near the N terminus <ref name="Versatile"/>.<br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain <ref name="Versatile"/><br /> <br /> <br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388197 User:Stephanie Maung/Sandbox 2012-05-04T20:05:10Z

<p>Stephanie Maung: </p> <hr /> <div>Outer Surface Protein B (OspB) has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = Background =<br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>H-6831-free</scene> and <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>H-6831 bound</scene> (residues 157-201) forms of OspB, some changes result from proteolysis near the N terminus <ref name="Versatile"/>.<br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain <ref name="Versatile"/><br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab <ref>PMID: 9038292 </ref>.<br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388192 User:Stephanie Maung/Sandbox 2012-05-04T19:58:52Z

<p>Stephanie Maung: </p> <hr /> <div>Outer Surface Protein B (OspB) has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = Background =<br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>backbone</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>lys</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388105 User:Stephanie Maung/Sandbox 2012-05-04T18:17:38Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>backbone</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/5'>loops</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>lys</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388090 User:Stephanie Maung/Sandbox 2012-05-04T18:01:58Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>backbone</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/4'>TextToBeDisplayed</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>lys</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388088 User:Stephanie Maung/Sandbox 2012-05-04T17:54:54Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/2'>loops</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/3'>lys</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1388085 User:Stephanie Maung/Sandbox 2012-05-04T17:47:23Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/2'>loops</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_lys_region_loops/1'>lys</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1387995 User:Stephanie Maung/Sandbox 2012-05-04T14:03:46Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/2'>loops</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_lys_region_loops/1'>lys</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1387991 User:Stephanie Maung/Sandbox 2012-05-04T13:57:34Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/2'>loops</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_trunc_region_loops_lys/1'>lys and loops</scene><br /> <br /> <br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1387877 User:Stephanie Maung/Sandbox 2012-05-04T06:11:15Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_loops/1'>loops</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_trunc_region_loops_lys/1'>lys and loops</scene><br /> <br /> <br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1387868 User:Stephanie Maung/Sandbox 2012-05-04T05:36:28Z

<p>Stephanie Maung: </p> <hr /> <div>= OspB Background =<br /> <br /> Lyme disease, discovered in 1975, is spread by means of a tick vector that carries the causative agent, spirochete [http://en.wikipedia.org/wiki/Borrelia_burgdorferi ''Borrelia Burgdorferi''] <ref name="Structural">PMID:15864264</ref>. It is the most frequently reported vectorborne illness in the United States. Individuals who have this disease may show symptoms including skin lesions called erythema migans and the characteristic bulls-eye rash <ref>http://www.cdc.gov/lyme/stats/index.html</ref>. OspA and OspB are the major outer surface proteins found on ''B. Borrelia''. OspB has shown significant variability in amino acid sequence and antigen reactivity in comparison to OspA, known to be largely invariant <ref name="Versatile">PMID:15713683</ref>. OspB has been found to play a vital role in the adherence of B. bugdorferi onto tick guts, which promote the survival of the vector and spread of Lyme disease. OspB-deficient B. budgdorferi have been found to bind poorly to tick gut extracts <ref>PMID: 17352535 </ref>.<br /> <br /> = OspB Interaction with Fab of H6831 =<br /> <br /> <Structure load='1rjl' size='450' frame='true' align='right' caption='OspB interacting with Fab H6831' scene='User:Olivia_Cheng/Sandbox_1/http://www.proteopedia.org/wiki/skins/common/images/button_headline.png1rjl_color/1' /><br /> <br /> The [http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Outer_surface_proteins outer-surface proteins] (Osps) in ''B. burgdorferi'' spirochete activate the classical and alternative pathways of the complement system. B. burgdorferi is resistant to complement mediated lysis. The complement inhibitor factor H binds to Osps and the C3b cascade is deactivated <ref name="Versatile"/>.<br /> <br /> Within this complex is <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_transparentabd/6'>a truncated form of OspB</scene>, shown in purple. The H6831 Fab is shown in white. (Click <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_color/1'>here</scene> to revert back to the original.)<br /> <br /> <br /> == H6831 ==<br /> <br /> H6831 is an IgG class monoclonal complement-independent antibody shown to effectively lyse outer surface protein B (OspB) of ''B. burgdorferi''. H6831 recognizes <scene name='User:Olivia_Cheng/Sandbox_1/1rjl_chainc_lys253/6'>Lys-253</scene> on OspB. Studies have shown that ''B. burgdorferi'' strains with Thr, Cys, Gly, or Glu instead of Lys decrease the binding affinity between H6831 and OspB <ref name="Versatile"/>.<br /> <br /> Due to its effective bactericidal actions, H6831 is used to generate less virulent escape variants of ''B. burgdorferi'' <ref name="Versatile"/>. In the majority of the mutations created from in vivo and in vitro immunization of mice, truncated forms of OspB within the C terminus lead to premature stop codons<ref>PMID:8308101 </ref>. It has been suggested that OspB mutants are more sensitive to proteolysis due to missense mutations that disturb the conformation of OspB <ref name="Versatile"/>. Truncated OspBs cease within the two C-terminal beta-strands of the central sheet. H6831 disorders or removes a beta sheet from OspB after binding. Cleavage may be a possible explanation for the conformational changes of OspB <ref>PMID:9125579</ref>.The sequence and structure of bactericidal H6831 Fab are typical for IgG2 heavy chain/kappa light chain class. In H6831 free and bound forms, some changes result from proteolysis near the N terminus. <ref name="Versatile"/><br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> == Binding ==<br /> <Structure load='1p4p' size='300' frame='true' align='right' caption='Residues 157 - 201 contain the cleaved region, shown in plum color.' scene='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2' /><br /> <br /> <Structure load='1rjl' size='300' frame='true' align='right' caption='The truncated version of OspB upon interaction with H6831' scene='User:Olivia_Cheng/workbench/1rjl_justc_gray/2' /><br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at <scene name='User:Olivia_Cheng/workbench/Loops_centered/1'>three exposed adjacent loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1 (medium orchid),2 (tomato) and 3 (light sea green). When binding of full-length OspB to Fab fragments of H6831 or CB2 fail, it is usually because <scene name='User:Olivia_Cheng/workbench/Loops_lysine_centered/3'>Lys-253</scene>, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times. <ref name="Versatile"/><br /> <br /> <br /> Aromatic residues tyrosine and tryptophan are also present in the OspB-H6831 interaction, a feature found in many antigen-antibody complexes. The Lys-253 residue forms a trans conformation between these aromatic residues of H6831. In the complex structure of the antibody binding site, the electron density is well defined and shows increased contact between Lys-253 and the antigen-binding site of the Fab. Most of the electrostatic and hydrogen-bond interactions occur between loop 2 and the Fab heavy chain. <br /> <br /> <br /> The H6831 epitope of OspB is topologically equivalent to LA-2 epitope of OspA <ref name="Versatile"/>. Similar to the LA-2 epitope, the H6831 epitope is positioned opposite the N-terminus near the end of the antigen. The buried surface area of OspB in the H6831 Fab complex is smaller than that of the OspA-LA2 complex. Loop 1 in the OspA-LA2 complex has the most interactions with the Fab, where as Loop 1 in the OspB-H6831 complex has the fewest interactions with the Fab. <ref>PMID: 9038292 </ref><br /> <br /> = Potential Mechanisms of Lysis =<br /> <br /> <br /> <br /> == Potential Catalytic Triad ==<br /> <br /> <Structure load='1p4p' size='250' frame='true' align='left' caption='OspB' scene='Insert optional scene name here' /><br /> <br /> [[Image: Cataly.png|300px|right|thumb| Comparison of catalytic triads]]<br /> <br /> The mechanism by which H6831 Fab destroys a spirochete appears to be a novel interaction. It is possible that Fab binding changes the properties of OspB folding, which may increase sensitivity of the protein to proteolysis or aggregation. NMR methods showed that the effects of binding can be propagated to regions of the antigen that are distant from epitope.” OspB shows signs of truncation after interacting with Fab of H6831 <ref>PMID: 1382591</ref>.<br /> <br /> It is possible that OspB performs an autoproteolysis. There is a <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_cat_triad_cool/9'>set of three residues</scene> found on OspB that resembles the catalytic triad of [[Serine_Proteases]]. This "constellation" consists of Thr-166, Arg-162, and Glu-184, which is similar to the catalytic triad residues of the serine protease [[trypsin]], which are Ser-195, His-57, Asp-102.<br /> <br /> Threonine and Glutamic acid are found in other catalytic triads of the serine hydrolase family, but argenine seems unlikely to replace histidine as a base because of its higher pKa. There have been studies that have shown that Argenine is essential for other enzymatic functions, such as in the Ser-Arg-Asp triad in cytosolic phospholipase A2 and as a catalytic base in Sortase A. <scene name='User:Olivia_Cheng/Sandbox_1/1p4p_asn164/1'>Asn-164</scene> forms an H-bond with Thr-166 and may rearrange to form a putative oxyanion hole with Thr-166 and another unidentified atom if active in the catalysis.<br /> <br /> <br /> <br /> == Potential Oxidative Mechanism ==<br /> <br /> It was recently discovered that all antibodies contained Fab portions that catalyzed a reaction between singlet oxygen and water, yielding hydrogen peroxide, ozone, water and hydroxide radicals. Hydrogen peroxide is a toxic oxidative species and might be the product of an ancient mechanism to protect against infection. UV absorption increases the rate for this reaction. B. burgdorferi is especially vulnerable to oxidative damage because its ecological niche is in areas with limited oxygen and its genome does not encode a catalase. This oxidative mechanism might explain why some mABs are bactericidal without the use of complement.<br /> <br /> = 3D Structures =<br /> <br /> [[Monoclonal_Antibody]]<br /> <br><br /> [[Trypsin]]<br /> <br /> = Links = <br /> <br /> *[cdc.gov/lyme] - the Official Lyme Disease resource of the US Center for Disease Control.<br /> <br /> = References =<br /> <br /> <references /><br /> <br /> <br /> <br /> <Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1387528 User:Stephanie Maung/Sandbox 2012-05-03T08:35:06Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>reset</scene><br /> <br /> H6831 Fab complex binds to a highly accessible region near the C-terminus of OspB, away from the N-terminus lipid anchor. The Fab makes contact at three exposed, adjacent <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops</scene>. The interaction of OspB-Fab complex depends heavily on hydrogen bonding between loops 1,2 and 3. When binding of full-length OspB and Fab fragments of H6831 or CB2 fail, it is usually because lys-253, located on loop 2, has been replaced with a different residue. Studies show that substitutions in basic residues of hen egg-white lysozyme (HEL) that participate in HEL-Fab complexes decreased binding affinity by 400-10,000 times.<br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1387468 User:Stephanie Maung/Sandbox 2012-05-03T04:01:50Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin</scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/2'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops 1,2, and 3</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1381485 User:Stephanie Maung/Sandbox 2012-04-26T19:13:33Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin</scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_253_triad_backbone/1'>backbone</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine_centered/1'>loops 1,2, and 3</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1381468 User:Stephanie Maung/Sandbox 2012-04-26T18:49:13Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin</scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_253_triad_backbone/1'>backbone</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Loops_lysine/1'>loops 1, 2 and 3</scene><br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377514 User:Stephanie Maung/Sandbox 2012-04-19T19:32:29Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin</scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_253_triad_backbone/1'>backbone</scene><br /> <br /> <br /> http://proteopedia.org/wiki/index.php/Serine_Proteases</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377510 User:Stephanie Maung/Sandbox 2012-04-19T19:29:31Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='center' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin</scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_253_triad_backbone/1'>backbone</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377508 User:Stephanie Maung/Sandbox 2012-04-19T19:22:48Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin</scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_253_triad_backbone/1'>backbone</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377503 User:Stephanie Maung/Sandbox 2012-04-19T19:09:36Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin</scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/1'>blah</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377502 User:Stephanie Maung/Sandbox 2012-04-19T19:08:57Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/Gray_1p4p/1'>origin/scene><br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>zoomed triad</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/1'>blah</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377500 User:Stephanie Maung/Sandbox 2012-04-19T19:07:09Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/2'>cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_triadzoom/1'>TextToBeDisplayed</scene><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/1'>zoomed triad</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377496 User:Stephanie Maung/Sandbox 2012-04-19T18:59:37Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='User:Stephanie_Maung/Sandbox/Gray_1p4p/1' /><br /> <br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/1'>catalytic triad and cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/1'>TextToBeDisplayed</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377495 User:Stephanie Maung/Sandbox 2012-04-19T18:57:07Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='Insert optional scene name here' /><br /> <br /> <br /> Residues 157 - 201 contain the <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/1'>catalytic triad and cleaved region</scene> of OspB upon interaction with Fab H6831.<br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/1'>TextToBeDisplayed</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377488 User:Stephanie Maung/Sandbox 2012-04-19T18:53:21Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='Insert optional scene name here' /><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/1'>1p4p_protelysed region and catalytic triad</scene><br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_triad_backbon/1'>TextToBeDisplayed</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377482 User:Stephanie Maung/Sandbox 2012-04-19T18:46:41Z

<p>Stephanie Maung: </p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='Insert optional scene name here' /><br /> <br /> <br /> <scene name='User:Stephanie_Maung/Sandbox/1p4p_proteolysed_region_triad/1'>1p4p_protelysed region and catalytic triad</scene></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung/Sandbox&diff=1377473 User:Stephanie Maung/Sandbox 2012-04-19T18:30:00Z

<p>Stephanie Maung: New page: <Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='Insert optional scene name here' /></p> <hr /> <div><Structure load='1P4P' size='500' frame='true' align='right' caption='Proteolysed Portion of OspB' scene='Insert optional scene name here' /></div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung&diff=1377464 User:Stephanie Maung 2012-04-19T18:00:50Z

<p>Stephanie Maung: </p> <hr /> <div>*Stephanie Maung<br /> *Undergraduate student at Stony Brook University <br /> *Stony Brook, New York USA<br /> *Biology major<br /> <br /> [[user: Olivia Cheng/workbench]]<br /> [[user: Stephanie Maung/Sandbox]]</div>

Stephanie Maung https://proteopedia.org/index.php?title=User:Stephanie_Maung&diff=1348542 User:Stephanie Maung 2012-02-02T20:43:55Z

<p>Stephanie Maung: </p> <hr /> <div>*Stephanie Maung<br /> *Undergraduate student at Stony Brook University <br /> *Stony Brook, New York USA<br /> *Biology major<br /> <br /> [[user: Olivia Cheng/workbench]]</div>

Stephanie Maung