Sandbox Reserved 779: Difference between revisions

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Post-translational modification : Alternate disulfide bonds occur in equal amounts in all variants examined.

Allergenic properties:Causes an allergic reaction in human. Is one of the causes of cow's milk allergy.

~~Miscellaneous The B variant sequence is shown.~~

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The lipocalin family is a large and diverse family of proteins with functions varying from insect camouflage to small hydrophobic molecule transport typified by the serum retinol-binding protein <ref>http://www.biochemj.org/bj/318/bj3180001.htm</ref>~~(http://www.biochemj.org/bj/318/0001/3180001.pdf).~~ The crystal structures so far determined reveal the typical lipocalin to be an eight-stranded antiparallel β-barrel arranged to form a conical central calyx or cavity in which the hydrophobic ligand is located.<ref>PMID:6540172</ref>

The lipocalin family is a large and diverse family of proteins with functions varying from insect camouflage to small hydrophobic molecule transport typified by the serum retinol-binding protein <ref>http://www.biochemj.org/bj/318/bj3180001.htm</ref> The crystal structures so far determined reveal the typical lipocalin to be an eight-stranded antiparallel β-barrel arranged to form a conical central calyx or cavity in which the hydrophobic ligand is located.<ref>PMID:6540172</ref>

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~~overall description of the structure of the protein:~~

~~a. oligomeric state~~

~~b. description of secondary structure~~

~~c. description of active residues of the protein and where they are on the protein~~

~~d. description of any ligands in the structure~~

~~e. methods used to solve the structure : X-ray crystallography, NMR, EM~~

βLG consists of 162 amino acid residues (18 kDa), containing two disulfide bonds (Cys 66–Cys 160 and Cys 106–Cys 119) and a free thiol (Cys 121). Structures of βLG have been reported by several groups with X-ray crystallography [19–21] and solution NMR [29,40,41]. It is a predominantly β-sheet protein. The β-barrel, or so called calyx, is conical and is made of two β-sheets: the B–D strands and N-terminal half of the A strand (denoted AN) form one sheet, and the E–H strands and C-terminal half of the A strand (denoted AC)form the other. On the outer surface of the β-barrel, between the G and H strands, is the 3-turn α-helix. The loops that connect the β-strands at the closed end of the calyx, BC, DE, and FG,are generally quite short, whereas those at the open end, AB, CD, EF,and GH, are significantly longer and more flexible [19]. In the calyx,there is a large central cavity which is surrounded by hydrophobic residues and is accessible to solvent. This cavity provides the principal ligand-binding site. βLG contains two tryptophan residues,Trp 19 on the A strand and Trp 61 on the C strand. The former is buried in the hydrophobic core whereas the latter is exposed to the solvent in the native structure, making them useful probes for monitoring site-specific conformational changes. In addition, studies on the monomer–dimer equilibrium [30,32,42,43] and the reactivity of the thiol group of Cys121 deeply buried between the α-helix and H strand [44–48] revealed other important properties of βLG.<ref>PMID:19362581</ref> the stability of the structure should depend so heavily upon the external loop around residue 64 or the beta strand with the free thiol<ref>PMID:9115437</ref>

At physiological conditions, bovine b-lactoglobulin forms a dimer, with each monomer consisting of 162 amino acid residues and characterized by a molecular mass of 18,350. Below pH 3, the dimer dissociates into <scene name='56/564055/Native_beta-lactoglobulin/1'>monomers</scene> which preserve their native conformation. Genetically, b-lactoglobulin may exist as one of several variants, among which the variants A and B are the most abundant. The A and B variants of the protein differ from each other by amino acid residues at positions Asp64 (Gly64 in variant B) and Val118 (Ala118 in variant B). These differences in primary structure render the two variants slightly different with respect to isoelectric point, solubility, self-association properties, as well as pressure and temperature stability. However, the structural characteristics of the A and B variants of bovine b-lactoglobulin are virtually indistinguishable. In its native state, b-lactoglobulin is a predominantly b-sheet protein containing nine b-strands and three a-helices. The core of the protein is formed by a flattened b-barrel (a calyx) composed of eight antiparallel b-strands (A to H).<ref>PMID:11734004</ref>

~~βLG consists~~ of ~~162 amino acid residues (18 kDa)~~, ~~containing two disulfide bonds (Cys 66–Cys 160 and Cys 106–Cys 119) and a free thiol (Cys 121). Structures~~ of ~~βLG have been reported by several groups with X-ray crystallography [19–21]~~ and ~~solution NMR~~ [29,~~40,41~~] ~~(Fig. 1A)~~. It is a ~~predominantly β-sheet protein. The β-barrel~~, ~~or so called calyx~~, ~~is conical and is made~~ of ~~two β~~-~~sheets:~~ the ~~B–D strands and N-terminal half~~ of the A strand (denoted AN) form one sheet, and the E–H strands and C-terminal half of the A strand (denoted AC)form the other (Fig. 1B). On the outer surface of the β-barrel, between the G and H strands, is the 3~~-turn α-helix~~. The ~~loops that connect the β-strands at the closed end~~ of the calyx~~, BC, DE,~~ and ~~FG,are generally quite short, whereas those at the open end, AB, CD, EF,and GH, are significantly longer and more flexible~~ [19]. ~~In the calyx,there is a large central cavity which is surrounded by hydrophobic residues and is accessible to solvent. This cavity provides the principal ligand~~-~~binding site. βLG~~ contains two ~~tryptophan residues~~,~~Trp 19 on the A strand~~ and ~~Trp 61 on the C strand. The former~~ is ~~buried in the hydrophobic core whereas the latter~~ is ~~exposed to the~~

Ligands

~~solvent in the native structure, making them useful probes for monitoring site-specific conformational changes. In addition, studies on the monomer–dimer equilibrium~~ [~~30,32,42,43~~] ~~and the reactivity of the thiol group of Cys121 deeply buried between the α-helix and H strand [44–48] revealed other important properties of βLG~~.<ref>PMID:~~19362581~~</ref>

Most lipocalins bind small hydrophobic molecules within the central cup or calyx. The true function of b-Lg is unknown, but it has been suggested that it is involved in

the transport of retinol and/or fatty acids [8,50]. It binds retinol with a higher affinity than does RBP [51] and, as with RBP, specific binding of retinol to b-Lg has been observed in the small intestine of the neonatal calf [3]. The structure of RBP with retinol bound within the hydrophobic calyx has been solved [2] and retinol was successfully modelled into our previous b-Lg structure [3].b-Lg contains two tryptophans, Trp19 and Trp61, and their fluorescence is altered when retinol is bound [51].<ref>PMID:9115437</ref>

~~===secondary structure elements===~~

~~protein fold and how thats important for the function~~

~~ligands if theres ligands~~

~~the active site if relevant~~

~~features of protein that are important for function~~

~~zoom in on the active site, label the important active site residues, and highlight those residues in a different color (make it look pretty)~~

==Mechanism of action==

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===Molecular mechanism of the Tanford transition===

Above pH 6.5, b-lactoglobulin undergoes the so-called Tanford transition which is triggered by protonation of Glu89 exhibiting an anomalously

high pKa value. The Tanford transition involves displacement of the loop EF (residues 85 to 90) that acts as a lid which closes the protein interior/binding site below pH 7.3 and opens it at higher pH. The Tanford transition may involve some other structural changes as well. For example, the transition is accompanied by a change in the microenvironment of Tyr428 and causes an alteration in the relative orientation of monomers in the dimer by as much as 5 degrees. It should be noted that all transitions that take place between pH 2 and pH 9 do not cause any appreciable changes in the nativelike b-barrel conformation of b-lactoglobulin.

high pKa value. The Tanford transition involves displacement of the loop EF (residues 85 to 90) that acts as a lid which closes the protein interior/binding site below pH 7.3 and opens it at higher pH. The Tanford transition may involve some other structural changes as well. For example, the transition is accompanied by a change in the microenvironment of Tyr428 and causes an alteration in the relative orientation of monomers in the dimer by as much as 5 degrees, which breaks a number of intersubunit hydrogen bonds. It should be noted that all transitions that take place between pH 2 and pH 9 do not cause any appreciable changes in the nativelike b-barrel conformation of b-lactoglobulin.

Sandbox Reserved 779: Difference between revisions

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@@ Line 23: / Line 23: @@
 Post-translational modification	: Alternate disulfide bonds occur in equal amounts in all variants examined.
 Allergenic properties:Causes an allergic reaction in human. Is one of the causes of cow's milk allergy.
-Miscellaneous	The B variant sequence is shown.
@@ Line 48: / Line 47: @@
 <ref>PMID:11058743</ref>
-The lipocalin family is a large and diverse family of proteins with functions varying from insect camouflage to small hydrophobic molecule transport typified by the serum retinol-binding protein <ref>http://www.biochemj.org/bj/318/bj3180001.htm</ref>(http://www.biochemj.org/bj/318/0001/3180001.pdf). The crystal structures so far determined reveal the typical lipocalin to be an eight-stranded antiparallel β-barrel arranged to form a conical central calyx or cavity in which the hydrophobic ligand is located.<ref>PMID:6540172</ref>
+The lipocalin family is a large and diverse family of proteins with functions varying from insect camouflage to small hydrophobic molecule transport typified by the serum retinol-binding protein <ref>http://www.biochemj.org/bj/318/bj3180001.htm</ref> The crystal structures so far determined reveal the typical lipocalin to be an eight-stranded antiparallel β-barrel arranged to form a conical central calyx or cavity in which the hydrophobic ligand is located.<ref>PMID:6540172</ref>
 <ref>PMID:9867826</ref>
@@ Line 54: / Line 53: @@
 <Structure load='1beb' size='400' frame='true' align='right' caption='β-Lactoglobulin (β-LG) (variant A)' scene='Insert optional scene name here' />
-overall description of the structure of the protein:
-a. oligomeric state
-b. description of secondary structure
-c. description of active residues of the protein and where they are on the protein
-d. description of any ligands in the structure
-e. methods used to solve the structure : X-ray crystallography, NMR, EM
+βLG consists of 162 amino acid residues (18 kDa), containing two disulfide bonds (Cys 66–Cys 160 and Cys 106–Cys 119) and a free thiol (Cys 121). Structures of βLG have been reported by several groups with X-ray crystallography [19–21] and solution NMR [29,40,41]. It is a predominantly β-sheet protein. The β-barrel, or so called calyx, is conical and is made of two β-sheets: the B–D strands and N-terminal half of the A strand (denoted AN) form one sheet, and the E–H strands and C-terminal half of the A strand (denoted AC)form the other. On the outer surface of the β-barrel, between the G and H strands, is the 3-turn α-helix. The loops that connect the β-strands at the closed end of the calyx, BC, DE, and FG,are generally quite short, whereas those at the open end, AB, CD, EF,and GH, are significantly longer and more flexible [19]. In the calyx,there is a large central cavity which is surrounded by hydrophobic residues and is accessible to solvent. This cavity provides the principal ligand-binding site. βLG contains two tryptophan residues,Trp 19 on the A strand and Trp 61 on the C strand. The former is buried in the hydrophobic core whereas the latter is exposed to the solvent in the native structure, making them useful probes for monitoring site-specific conformational changes. In addition, studies on the monomer–dimer equilibrium [30,32,42,43] and the reactivity of the thiol group of Cys121 deeply buried between the α-helix and H strand [44–48] revealed other important properties of βLG.<ref>PMID:19362581</ref> the stability of the structure should depend so heavily upon the external loop around residue 64 or the beta strand with the free thiol<ref>PMID:9115437</ref>
 At physiological conditions, bovine b-lactoglobulin forms a dimer, with each monomer consisting of 162 amino acid residues and characterized by a molecular mass of 18,350. Below pH 3, the dimer dissociates into <scene name='56/564055/Native_beta-lactoglobulin/1'>monomers</scene> which preserve their native conformation. Genetically, b-lactoglobulin may exist as one of several variants, among which the variants A and B are the most abundant. The A and B variants of the protein differ from each other by amino acid residues at positions Asp64 (Gly64 in variant B) and Val118 (Ala118 in variant B). These differences in primary structure render the two variants slightly different with respect to isoelectric point, solubility, self-association properties, as well as pressure and temperature stability. However, the structural characteristics of the A and B variants of bovine b-lactoglobulin are virtually indistinguishable. In its native state, b-lactoglobulin is a predominantly b-sheet protein containing nine b-strands and three a-helices. The core of the protein is formed by a flattened b-barrel (a calyx) composed of eight antiparallel b-strands (A to H).<ref>PMID:11734004</ref>
-βLG consists of 162 amino acid residues (18 kDa), containing two disulfide bonds (Cys 66–Cys 160 and Cys 106–Cys 119) and a free thiol (Cys 121). Structures of βLG have been reported by several groups with X-ray crystallography [19–21] and solution NMR [29,40,41] (Fig. 1A). It is a predominantly β-sheet protein. The β-barrel, or so called calyx, is conical and is made of two β-sheets: the B–D strands and N-terminal half of the A strand (denoted AN) form one sheet, and the E–H strands and C-terminal half of the A strand (denoted AC)form the other (Fig. 1B). On the outer surface of the β-barrel, between the G and H strands, is the 3-turn α-helix. The loops that connect the β-strands at the closed end of the calyx, BC, DE, and FG,are generally quite short, whereas those at the open end, AB, CD, EF,and GH, are significantly longer and more flexible [19]. In the calyx,there is a large central cavity which is surrounded by hydrophobic residues and is accessible to solvent. This cavity provides the principal ligand-binding site. βLG contains two tryptophan residues,Trp 19 on the A strand and Trp 61 on the C strand. The former is buried in the hydrophobic core whereas the latter is exposed to the
+Ligands
-solvent in the native structure, making them useful probes for monitoring site-specific conformational changes. In addition, studies on the monomer–dimer equilibrium [30,32,42,43] and the reactivity of the thiol group of Cys121 deeply buried between the α-helix and H strand [44–48] revealed other important properties of βLG.<ref>PMID:19362581</ref>
+Most lipocalins bind small hydrophobic molecules within the central cup or calyx. The true function of b-Lg is unknown, but it has been suggested that it is involved in
+the transport of retinol and/or fatty acids [8,50]. It binds retinol with a higher affinity than does RBP [51] and, as with RBP, specific binding of retinol to b-Lg has been observed in the small intestine of the neonatal calf [3]. The structure of RBP with retinol bound within the hydrophobic calyx has been solved [2] and retinol was successfully modelled into our previous b-Lg structure [3].b-Lg contains two tryptophans, Trp19 and Trp61, and their fluorescence is altered when retinol is bound [51].<ref>PMID:9115437</ref>
-===secondary structure elements===
-protein fold and how thats important for the function
-ligands if theres ligands
-the active site if relevant
-features of protein that are important for function
-zoom in on the active site, label the important active site residues, and highlight those residues in a different color (make it look pretty)
 ==Mechanism of action==
@@ Line 81: / Line 67: @@
 ===Molecular mechanism of the Tanford transition===
 Above pH 6.5, b-lactoglobulin undergoes the so-called Tanford transition which is triggered by protonation of Glu89 exhibiting an anomalously
-high pKa value. The Tanford transition involves displacement of the loop EF (residues 85 to 90) that acts as a lid which closes the protein interior/binding site below pH 7.3 and opens it at higher pH. The Tanford transition may involve some other structural changes as well. For example, the transition is accompanied by a change in the microenvironment of Tyr428 and causes an alteration in the relative orientation of monomers in the dimer by as much as 5 degrees. It should be noted that all transitions that take place between pH 2 and pH 9 do not cause any appreciable changes in the nativelike b-barrel conformation of b-lactoglobulin.
+high pKa value. The Tanford transition involves displacement of the loop EF (residues 85 to 90) that acts as a lid which closes the protein interior/binding site below pH 7.3 and opens it at higher pH. The Tanford transition may involve some other structural changes as well. For example, the transition is accompanied by a change in the microenvironment of Tyr428 and causes an alteration in the relative orientation of monomers in the dimer by as much as 5 degrees, which breaks a number of intersubunit hydrogen bonds. It should be noted that all transitions that take place between pH 2 and pH 9 do not cause any appreciable changes in the nativelike b-barrel conformation of b-lactoglobulin.
 <ref>PMID:11734004</ref>