1hfm: Difference between revisions
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< | ==A THREE-DIMENSIONAL MODEL OF AN ANTI-LYSOZYME ANTIBODY== | ||
The | <StructureSection load='1hfm' size='340' side='right'caption='[[1hfm]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HFM FirstGlance]. <br> | |||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hfm FirstGlance], [https://www.ebi.ac.uk/pdbsum/1hfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hfm ProSAT]</span></td></tr> | |||
- | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The primary amino acid structure of the lysozyme-binding antibody, HyHEL-10, as determined by amino acid and nucleotide sequencing was utilized to construct a scale model of the Fv (variable region domain of immunoglobulin) using energy-minimized torsional angles of the McPC603 Fv as a prototype template. This model was in turn used as a template for generating a computer-built set of co-ordinates, which were subjected to a total of 600 steps of Adopted Basis Newton-Raphson energy minimizations using the program CHARMM. Only minimal shifts of the backbone (root-mean-square 0.76 A) were required to give an energetically stable structure with a favorable van der Waals' energy. Several notable features were evident from both the scale model and the energy-minimized computer model: (1) the shape of the antibody combining region is that of a very shallow concavity approximately 20 A X 25 A; (2) the concavity is acidic and non-hydrophobic and is bordered by hydrophobic segments; (3) the lower portion of the combining site is dominated by a cluster of tyrosine residues over the L3 and H2 areas; (4) a somatic mutation encoded by the J region of the heavy chain (JH) may contribute significantly to the complementarity of heavy chain H3 to the epitope on hen egg white lysozyme. In addition, the space-filling energy-minimized model revealed that residue 49L, a framework residue, was prominently exposed and accessible in the center of the combining-site concavity. The model suggests that variation in length of complementarity-determining regions may function not only to change directly the shape of the antibody combining site, but may also influence indirectly the nature of the antibody surface by changing the accessibility of residues not usually involved in antigen binding. | |||
A three-dimensional model of an anti-lysozyme antibody.,Smith-Gill SJ, Mainhart C, Lavoie TB, Feldmann RJ, Drohan W, Brooks BR J Mol Biol. 1987 Apr 20;194(4):713-24. PMID:3656404<ref>PMID:3656404</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1hfm" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Theoretical Model]] | ||
[[Category: Large Structures]] | |||
== | |||
< | |||
[[Category: Brooks, B R]] | [[Category: Brooks, B R]] | ||
[[Category: Drohan, W]] | [[Category: Drohan, W]] | ||
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[[Category: Mainhart, C]] | [[Category: Mainhart, C]] | ||
[[Category: Smith-Gill, S J]] | [[Category: Smith-Gill, S J]] | ||
Latest revision as of 13:49, 4 August 2021
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A THREE-DIMENSIONAL MODEL OF AN ANTI-LYSOZYME ANTIBODYA THREE-DIMENSIONAL MODEL OF AN ANTI-LYSOZYME ANTIBODY
Structural highlights
Publication Abstract from PubMedThe primary amino acid structure of the lysozyme-binding antibody, HyHEL-10, as determined by amino acid and nucleotide sequencing was utilized to construct a scale model of the Fv (variable region domain of immunoglobulin) using energy-minimized torsional angles of the McPC603 Fv as a prototype template. This model was in turn used as a template for generating a computer-built set of co-ordinates, which were subjected to a total of 600 steps of Adopted Basis Newton-Raphson energy minimizations using the program CHARMM. Only minimal shifts of the backbone (root-mean-square 0.76 A) were required to give an energetically stable structure with a favorable van der Waals' energy. Several notable features were evident from both the scale model and the energy-minimized computer model: (1) the shape of the antibody combining region is that of a very shallow concavity approximately 20 A X 25 A; (2) the concavity is acidic and non-hydrophobic and is bordered by hydrophobic segments; (3) the lower portion of the combining site is dominated by a cluster of tyrosine residues over the L3 and H2 areas; (4) a somatic mutation encoded by the J region of the heavy chain (JH) may contribute significantly to the complementarity of heavy chain H3 to the epitope on hen egg white lysozyme. In addition, the space-filling energy-minimized model revealed that residue 49L, a framework residue, was prominently exposed and accessible in the center of the combining-site concavity. The model suggests that variation in length of complementarity-determining regions may function not only to change directly the shape of the antibody combining site, but may also influence indirectly the nature of the antibody surface by changing the accessibility of residues not usually involved in antigen binding. A three-dimensional model of an anti-lysozyme antibody.,Smith-Gill SJ, Mainhart C, Lavoie TB, Feldmann RJ, Drohan W, Brooks BR J Mol Biol. 1987 Apr 20;194(4):713-24. PMID:3656404[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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