Proteopedia - User contributions [en]

User:Marvin O'Neal/Antibody OspA and OspB

2012-04-30T01:48:45Z

Alexandros Konstantinidis:

==Introduction==
===''Borrelia burgdoferi''===

The causative agent of [http://en.wikipedia.org/wiki/Lyme_disease Lyme disease] is ''[http://en.wikipedia.org/wiki/Borrelia_burgdorferi Borellia burgdorferi]'', a [http://en.wikipedia.org/wiki/Spirochaete spirochaete] found in the gut of hard bodied ticks of genus ''[http://en.wikipedia.org/wiki/ Ixodes]''. A factor contributing to the severity of Lyme disease is its resistance to certain forms of complement-dependent immune response by the evasion of the [http://en.wikipedia.org/wiki/Alternative_complement_pathway alternative complement pathway] and the blocking of complement [http://en.wikipedia.org/wiki/Complement_component_3 C3]. <ref>PMID:18080415</ref> This resistance increases the importance of the complement independent immune response when combating ''B. burgdorferi''. Certain fragment antigen binding regions ([http://en.wikipedia.org/wiki/Fragment_antigen-binding fab]) of IgG and IgM monoclonal antibodies are bactericidal even in the absence of complement. Binding of these fabs to their corresponding outer surface protein (OspA and OspB) of ''B. burgdoferi'' leads to the lysis of the bacteria.<ref>PMID:15864264</ref>

===Fragment Antigen Binding (fab) Reigon===
[[Image:Fab reigon.png|right|thumb|Digestion of an antibody by Papain separates the fab reigons from the antibody]]
Fab consists of a heavy and a light chain and each chain is composed of a variable and a constant region. The [http://en.wikipedia.org/wiki/Paratope paratope] is located in the N terminal of the variable region of the [http://en.wikipedia.org/wiki/Immunoglobulin_heavy_chain heavy chain] and [http://en.wikipedia.org/wiki/Immunoglobulin_light_chain light chain] of the fab. The complement-independent fab regions that interact with these outer surface proteins are LA-2, which targets the C-terminal of OspA, and CB2 and H6831, which target the C-terminal of OspB. <ref>PMID:107164</ref>

==OspB and H6831==
<Structure load='1RJL' size='400' frame='true' align='right' caption='OspB and H6831 Fab complex' scene='Studio:G1SecL01/1/10' />

===Complex Interaction between OspB and H6831===
<scene name='Studio:G1SecL01/1/10'>Restore Original Scene</scene>

The <scene name='Studio:G1SecL01/1/10'>OspB-H6831 complex</scene> consist of two main components, the outer surface protein <scene name='Studio:G1SecL01/1/11'>OspB</scene>, and the <scene name='Studio:G1SecL01/1/12'>fab</scene>, subdivided into the <scene name='Studio:G1SecL01/1/14'>heavy chain</scene> and the <scene name='Studio:G1SecL01/1/13'>light chain</scene>. Most hydrogen bonds and electrostatic interactions that are responsible for the binding of H6831 to OspB are between the <scene name='Studio:G1SecL01/1/15'>three adjacent surface-exposed loops</scene> at the C-terminal of OspB and some <scene name='Studio:G1SecL01/1/16'>residues</scene> on the fab heavy chain that include tyrosine, tryptophan, glutamate, and histidine.

The majority of the electrostatic and hydrogen-bonded interactions are between loop 2 (residues 250-254) and the fab heavy chain. <scene name='Studio:G1SecL01/1/17'>Lysine 253</scene> in loop 2 of OspB has a necessary and major role due to its central position in the exposed loops. A mutation at its position abrogates the binding interaction and causes the resistance of the bacteria to the bactericidal effect of the fab. Lys 253 binds to the two aromatic residues on the fab heavy chain, tyrosine (green link) and tryptophan (green link). It also makes hydrogen bonds with the glutamate (green link) in the heavy chain of the fab and forms an ionic bond. Carbonyl in loop 1 (green link) of the OspB interacts with histidine in the fab heavy chain. <scene name='Studio:G1SecL01/1/18'>Loop 3</scene> of OspB interacts with fab light chain. <ref name=becker>PMID:15713683</ref>.

===Conformational Changes to OspB===
The binding leads to some conformational changes in OspB. Whereas Ding et al.<ref name=ding>PMID:11183781</ref> found no changes in the C-terminal of OspA upon the binding to the fab. The most significant difference between the free and the complexed structure of OspB is the loss of the central <scene name='Studio:G1SecL01/1/19'>beta sheet</scene> strands 1-4. Both small positional shifts near the Fab binding site and a few larger structural changes away from the binding site were observed. The largest shifts (7– 8 Å) correspond to the repositioning of a loop opposite the Fab-binding site (residues 218 –220). In the free OspB structure, all regions that exhibit shifts are adjacent to the central sheet; in the OspB-H6831 complex they all shift toward, and slightly overlap, the position of the missing sheet. These observations suggest that the larger conformational changes are related to the loss of the central sheet, which could have happened through proteolytic cleavage or fortuitous crystal contacts <ref name=becker />.

====Requirements for the Bactericidal Effect and Proposed Mechanism====
The fab binding destabilizes the [http://en.wikipedia.org/wiki/Bacterial_outer_membrane outer membrane] (OM) of B. burdorferi, with subsequent formation of [http://en.wikipedia.org/wiki/Spheroplast spheroplasts]. It has been observed that the bactericidal action, but not the binding, requires the presence of bivalent cations (Mg2+ and Ca2+). Escudero et al. study demonstrated the inability of fab to kill bacteria in the absence of the bivalent cations. It was speculated that OspB- Cb2 (a fab similar to H6831) complexes could create physical openings in the OM allowing for rapid infusion of electrolytes, increasing the osmolarity of the periplasm and triggering bivalent cation dependent cascades <ref>Escudero; Halluska et al. 1997</ref>.
Need to be rephrased and squeezed and may be a sentence about the cholestrol needs to be added and if there is a specific function for the charge triad it may be added

==OspA and LA-2==
<Structure load='1FJ1' size='400' frame='true' align='right' caption='OspA-LA2 Complex' scene='Insert optional scene name here' />
===OspA===
OspA is 53% similar to OspB. OspA is usually undetectable in the early stages of lyme disease, because it is down regulated when OspC is expressed (provide citation). Despite the similarity between OspA and OspB, both in vivo and vitro OspB is susceptible to cleavage by exogenous [http://en.wikipedia.org/wiki/Protease proteases], whereas OspA is relatively resistant (Becker, structural). This characteristic may have contributed to OspA being a better vaccine to lyme disease that is used to prevent transmission of B.burgodorferi from tick vector to mammalian host by complement-independent killing.<ref name=ding />
===Interaction between OspA and LA-2===
LA-2 is an IgM murine monoclonal antibody that interacts with three exposed loop on the C-terminal of OspA. These interactions include eight direct hydrogen bonds, four solvent-bridged hydrogen bonds, three ion pairs, and numerous van der Waals interactions <ref name=ding />.
===Conformational changes===
Conformational changes upon the binding of OspA and LA-2 show that LA-2 recognition of OspA involves an induced fit mechanism where loops 1-3 conformations shift to optimize complementarity to the antigen-combining site <ref name=ding />. The overall structure of the C-terminal of OspA is unchanged upon the binding of LA-2 with comparison to the free OspA, except for the minor shift to accommodate for the binding. The maximum atomic shift is 4.7A at the site of Ser206.<ref>PMID: 11183781</ref>

<scene name='Studio:G1SecL01/1/10'>Restore Original Scene</scene>

References: {{reflist}}

User:Marvin O'Neal/Antibody OspA and OspB

2012-04-29T13:14:05Z

Alexandros Konstantinidis:

==Introduction==
===''Borrelia burgdoferi''===
A causative agent of Lyme disease is ''Borrelia burgdorferi'', a gram negative, helically coiled bacterium which belongs to the spirochete phylum. Antibodies play a versatile and important role in fighting the ''B. burgdoferi'' bacteria. ''B. burgdoferi'' can develop a resistance to certain forms of complement-dependent immune response by the evasion of the alternative complement pathway, and the blocking of complement C3. <ref>La Rocca and Benach 2008</ref> important diverse role of antibody. This resistance increases the importance of the complement independent immune response when combating ''Borrelia burgdorferi'' ''in vivo''. The fragment antigen binding reigons of IgG and IgM monoclonal antibodies to outer surface proteins (Osp) A and B of ''B. burgdoferi'' leads to a complement-independent lysis of the bacteria. <ref>Connolly and Benach 2005</ref>.

===Fragment Antigen Binding (fab) Reigon===
[[Image:Fab reigon.png|right|thumb|Digestion of an antibody by Papain separates the fab reigons from the antibody]]
The fragment antigen binding reigons, also known as fab reigons, consist of the light and N-terminus of the heavy chain of antibodies. There are two fab reigons per antibody, and each fab is composed of both a variable and constant reigon. The variable reigon contains the paratope (which binds to an antigen's epitope), located at the N terminus of both the heavy and light chains of the fab. The complement-independent fab reigons most pertienent to Lyme disease are IgG antibody fabs CB2 and H6831, which target the C-terminal of OspB, and ????? IgG LA2, which targets OspB in ''B. burgdoferi'' <ref>Putnam 1979</ref>.

==OspB and H6831==
<Structure load='1RJL' size='300' frame='true' align='right' caption='OspB and H6831 Fab complex' scene='Studio:G1SecL01/1/10' />
<scene name='Studio:G1SecL01/1/10'>Restore Original Scene</scene>
===Complex Interaction between OspB and H6831===
Fab-Osp complexes, such as the OspB-H6831 complex, consist of two main components; the <scene name='Studio:G1SecL01/1/11'>Outer Surface Protein</scene> (OspB in this case), and the <scene name='Studio:G1SecL01/1/12'>fab</scene>, which is subdivided into the <scene name='Studio:G1SecL01/1/14'>heavy chain</scene>, and the <scene name='Studio:G1SecL01/1/13'>light chain</scene>. Most hydrogen bonds and electrostatic interactions that are responsible for the binding of H6831 to OspB are between the three adjacent surface-exposed <scene name='Studio:G1SecL01/1/15'>loops</scene> at the C-terminal of OspB and some <scene name='Studio:G1SecL01/1/16'>residues</scene> on the fab heavy chain that include tyrosine, tryptophan, glutamate, and histidine. The majority of the electrostatic and hydrogen-bonded interactions are between loop 2 (residues 250-254) and the fab heavy chain. <scene name='Studio:G1SecL01/1/17'>Lysine 253</scene> in loop 2 of OspB has a necessary and major role due to its central position in the exposed loops. A mutation at its position abrogates the binding interaction and causes the resistance of the bacteria to the bactericidal effect of the fab. Lys 253 binds to the two aromatic residues on the fab heavy chain, tyrosine (green link) and tryptophan (green link). It also makes hydrogen bonds with the glutamate (green link) in the heavy chain of the fab. Carbonyl in loop 1 (green link) of the OspB interacts with histidine in the fab heavy chain. <scene name='Studio:G1SecL01/1/18'>Loop 3</scene> of OspB interacts with fab light chain. <ref>Becker; Bunikis et al. 2004</ref>.

===Conformational Changes to OspB===
The binding leads to some conformational changes in OspB. Whereas Ding et al.<ref>Ding et al</ref> found no changes in the C-terminal of OspA upon the binding to the fab. The most significant difference between the free and the complexed structure of OspB is the loss of the central <scene name='Studio:G1SecL01/1/19'>beta sheet</scene> strands 1-4. Both small positional shifts near the Fab binding site and a few larger structural changes away from the binding site were observed. The largest shifts (7– 8 Å) correspond to the repositioning of a loop opposite the Fab-binding site (residues 218 –220). In the free OspB structure, all regions that exhibit shifts are adjacent to the central sheet; in the OspB-H6831 complex they all shift toward, and slightly overlap, the position of the missing sheet. These observations suggest that the larger conformational changes are related to the loss of the central sheet, which could have happened through proteolytic cleavage or fortuitous crystal contacts <ref>Becker; Bunikis et al. 2004</ref>

====Requirements for the Bactericidal Effect and Proposed Mechanism====
The fab binding destabilizes the outer membrane (OM) of B. burdorferi, with subsequent formation of spheroplasts. It has been observed that the bactericidal action, but not the binding, requires the presence of bivalent cations (Mg2+ and Ca2+). Escudero et al. study demonstrated the inability of fab to kill bacteria in the absence of the bivalent cations. It was speculated that OspB- Cb2 (a fab similar to H6831) complexes could create physical openings in the OM allowing for rapid infusion of electrolytes, increasing the osmolarity of the periplasm and triggering bivalent cation dependent cascades <ref>Escudero; Halluska et al. 1997</ref>.
Need to be rephrased and squeezed and may be a sentence about the cholestrol needs to be added and if there is a specific function for the charge triad it may be added

==OspA and LA-2==
<Structure load='1FJ1' size='300' frame='true' align='right' caption='OspA-LA2 Complex' scene='Insert optional scene name here' />

==Temporary Stuff==

<scene name='Studio:G1SecL01/Complex_s/1'>original scene S</scene>

<scene name='Studio:G1SecL01/Loop_2_s/1'>Loop 2 S</scene>

<scene name='Studio:G1SecL01/Lys_253_s/1'>lys 253 S</scene>

IgG antibody fabs CB2 and <scene name='Studio:G1SecL01/1/9'>H6831</scene>are structurally similar and both target the C-terminal of <scene name='Studio:G1SecL01/1/2'>OspB</scene>. H6831 consists of a <scene name='Studio:G1SecL01/1/3'>light</scene> and a <scene name='Studio:G1SecL01/1/4'>heavy</scene> chain and each chain is composed of a variable and a constant domain. The paratope is located at the N terminal of the variable region of both the heavy and the light chains (Putnam 1979). Fab binding destabilizes the outer membrane (OM) of ''B. burdorferi'' with subsequent formation of spheroplasts. It has been observed that the bactericidal action upon binding requires the presence of bivalent cations (Mg2+ and Ca2+). When a similar fab, CB2, is bound to OspB, channels open in the OM allowing rapid infusion of electrolytes,increasing the osmolarity of the periplasm and triggering bivalent cation dependent cascades <ref>PMID:9125579</ref>

##When bound to a similar fab CB2, OspB-CB2 complexes could create physical openings in the OM allowing for rapid infusion of electrolytes, increasing the osmolarity of the periplasm and triggering bivalent cation dependent cascades <ref>Escudero; Halluska et al. 1997</ref>##

<scene name='Studio:G1SecL01/1/5'>three exposed loops</scene>

<scene name='Studio:G1SecL01/1/6'>Lysine 253</scene>

<scene name='Studio:G1SecL01/1/7'>Lysine 253 with crucial heavy chain amino acids</scene>

<scene name='Studio:G1SecL01/1/8'>B sheet that gets removed</scene>

References: {{reflist}}

User:Marvin O'Neal/Antibody OspA and OspB

2012-04-29T13:13:41Z

Alexandros Konstantinidis:

==Introduction==
===''Borrelia burgdoferi''===
A causative agent of Lyme disease is ''Borrelia burgdorferi'', a gram negative, helically coiled bacterium which belongs to the spirochete phylum. Antibodies play a versatile and important role in fighting the ''B. burgdoferi'' bacteria. ''B. burgdoferi'' can develop a resistance to certain forms of complement-dependent immune response by the evasion of the alternative complement pathway, and the blocking of complement C3. <ref>La Rocca and Benach 2008</ref> important diverse role of antibody. This resistance increases the importance of the complement independent immune response when combating ''Borrelia burgdorferi'' ''in vivo''. The fragment antigen binding reigons of IgG and IgM monoclonal antibodies to outer surface proteins (Osp) A and B of ''B. burgdoferi'' leads to a complement-independent lysis of the bacteria. <ref>Connolly and Benach 2005</ref>.

===Fragment Antigen Binding (fab) Reigon===
[[Image:Fab reigon.png|right|thumb|Digestion of an antibody by Papain separates the fab reigons from the antibody]]
The fragment antigen binding reigons, also known as fab reigons, consist of the light and N-terminus of the heavy chain of antibodies. There are two fab reigons per antibody, and each fab is composed of both a variable and constant reigon. The variable reigon contains the paratope (which binds to an antigen's epitope), located at the N terminus of both the heavy and light chains of the fab. The complement-independent fab reigons most pertienent to Lyme disease are IgG antibody fabs CB2 and H6831, which target the C-terminal of OspB, and ????? IgG LA2, which targets OspB in ''B. burgdoferi'' <ref>Putnam 1979</ref>.
dd

==OspB and H6831==
<Structure load='1RJL' size='300' frame='true' align='right' caption='OspB and H6831 Fab complex' scene='Studio:G1SecL01/1/10' />
<scene name='Studio:G1SecL01/1/10'>Restore Original Scene</scene>
===Complex Interaction between OspB and H6831===
Fab-Osp complexes, such as the OspB-H6831 complex, consist of two main components; the <scene name='Studio:G1SecL01/1/11'>Outer Surface Protein</scene> (OspB in this case), and the <scene name='Studio:G1SecL01/1/12'>fab</scene>, which is subdivided into the <scene name='Studio:G1SecL01/1/14'>heavy chain</scene>, and the <scene name='Studio:G1SecL01/1/13'>light chain</scene>. Most hydrogen bonds and electrostatic interactions that are responsible for the binding of H6831 to OspB are between the three adjacent surface-exposed <scene name='Studio:G1SecL01/1/15'>loops</scene> at the C-terminal of OspB and some <scene name='Studio:G1SecL01/1/16'>residues</scene> on the fab heavy chain that include tyrosine, tryptophan, glutamate, and histidine. The majority of the electrostatic and hydrogen-bonded interactions are between loop 2 (residues 250-254) and the fab heavy chain. <scene name='Studio:G1SecL01/1/17'>Lysine 253</scene> in loop 2 of OspB has a necessary and major role due to its central position in the exposed loops. A mutation at its position abrogates the binding interaction and causes the resistance of the bacteria to the bactericidal effect of the fab. Lys 253 binds to the two aromatic residues on the fab heavy chain, tyrosine (green link) and tryptophan (green link). It also makes hydrogen bonds with the glutamate (green link) in the heavy chain of the fab. Carbonyl in loop 1 (green link) of the OspB interacts with histidine in the fab heavy chain. <scene name='Studio:G1SecL01/1/18'>Loop 3</scene> of OspB interacts with fab light chain. <ref>Becker; Bunikis et al. 2004</ref>.

===Conformational Changes to OspB===
The binding leads to some conformational changes in OspB. Whereas Ding et al.<ref>Ding et al</ref> found no changes in the C-terminal of OspA upon the binding to the fab. The most significant difference between the free and the complexed structure of OspB is the loss of the central <scene name='Studio:G1SecL01/1/19'>beta sheet</scene> strands 1-4. Both small positional shifts near the Fab binding site and a few larger structural changes away from the binding site were observed. The largest shifts (7– 8 Å) correspond to the repositioning of a loop opposite the Fab-binding site (residues 218 –220). In the free OspB structure, all regions that exhibit shifts are adjacent to the central sheet; in the OspB-H6831 complex they all shift toward, and slightly overlap, the position of the missing sheet. These observations suggest that the larger conformational changes are related to the loss of the central sheet, which could have happened through proteolytic cleavage or fortuitous crystal contacts <ref>Becker; Bunikis et al. 2004</ref>

====Requirements for the Bactericidal Effect and Proposed Mechanism====
The fab binding destabilizes the outer membrane (OM) of B. burdorferi, with subsequent formation of spheroplasts. It has been observed that the bactericidal action, but not the binding, requires the presence of bivalent cations (Mg2+ and Ca2+). Escudero et al. study demonstrated the inability of fab to kill bacteria in the absence of the bivalent cations. It was speculated that OspB- Cb2 (a fab similar to H6831) complexes could create physical openings in the OM allowing for rapid infusion of electrolytes, increasing the osmolarity of the periplasm and triggering bivalent cation dependent cascades <ref>Escudero; Halluska et al. 1997</ref>.
Need to be rephrased and squeezed and may be a sentence about the cholestrol needs to be added and if there is a specific function for the charge triad it may be added

==OspA and LA-2==
<Structure load='1FJ1' size='300' frame='true' align='right' caption='OspA-LA2 Complex' scene='Insert optional scene name here' />

==Temporary Stuff==

<scene name='Studio:G1SecL01/Complex_s/1'>original scene S</scene>

<scene name='Studio:G1SecL01/Loop_2_s/1'>Loop 2 S</scene>

<scene name='Studio:G1SecL01/Lys_253_s/1'>lys 253 S</scene>

IgG antibody fabs CB2 and <scene name='Studio:G1SecL01/1/9'>H6831</scene>are structurally similar and both target the C-terminal of <scene name='Studio:G1SecL01/1/2'>OspB</scene>. H6831 consists of a <scene name='Studio:G1SecL01/1/3'>light</scene> and a <scene name='Studio:G1SecL01/1/4'>heavy</scene> chain and each chain is composed of a variable and a constant domain. The paratope is located at the N terminal of the variable region of both the heavy and the light chains (Putnam 1979). Fab binding destabilizes the outer membrane (OM) of ''B. burdorferi'' with subsequent formation of spheroplasts. It has been observed that the bactericidal action upon binding requires the presence of bivalent cations (Mg2+ and Ca2+). When a similar fab, CB2, is bound to OspB, channels open in the OM allowing rapid infusion of electrolytes,increasing the osmolarity of the periplasm and triggering bivalent cation dependent cascades <ref>PMID:9125579</ref>

##When bound to a similar fab CB2, OspB-CB2 complexes could create physical openings in the OM allowing for rapid infusion of electrolytes, increasing the osmolarity of the periplasm and triggering bivalent cation dependent cascades <ref>Escudero; Halluska et al. 1997</ref>##

<scene name='Studio:G1SecL01/1/5'>three exposed loops</scene>

<scene name='Studio:G1SecL01/1/6'>Lysine 253</scene>

<scene name='Studio:G1SecL01/1/7'>Lysine 253 with crucial heavy chain amino acids</scene>

<scene name='Studio:G1SecL01/1/8'>B sheet that gets removed</scene>

References: {{reflist}}