VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.
Many algorithms that compare protein structures can reveal similarities that suggest related biological functions, even at great evolutionary distances. Proteins with related function often exhibit differences in binding specificity, but few algorithms identify structural variations that effect spec...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2010-08-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC2930297?pdf=render |
| _version_ | 1819265201016406016 |
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| author | Brian Y Chen Barry Honig |
| author_facet | Brian Y Chen Barry Honig |
| author_sort | Brian Y Chen |
| collection | DOAJ |
| description | Many algorithms that compare protein structures can reveal similarities that suggest related biological functions, even at great evolutionary distances. Proteins with related function often exhibit differences in binding specificity, but few algorithms identify structural variations that effect specificity. To address this problem, we describe the Volumetric Analysis of Surface Properties (VASP), a novel volumetric analysis tool for the comparison of binding sites in aligned protein structures. VASP uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods. Our approach, inspired by techniques from constructive solid geometry, enables the isolation of volumetrically conserved and variable regions within three dimensionally superposed volumes. We applied VASP to compute a comparative volumetric analysis of the ligand binding sites formed by members of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains and the serine proteases. Within both families, VASP isolated individual amino acids that create structural differences between ligand binding cavities that are known to influence differences in binding specificity. Also, VASP isolated cavity subregions that differ between ligand binding cavities which are essential for differences in binding specificity. As such, VASP should prove a valuable tool in the study of protein-ligand binding specificity. |
| first_indexed | 2024-12-23T20:41:36Z |
| format | Article |
| id | doaj.art-c37cd1786ff540ba99bfe38693a0cb28 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-23T20:41:36Z |
| publishDate | 2010-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-c37cd1786ff540ba99bfe38693a0cb282022-12-21T17:31:54ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582010-08-016810.1371/journal.pcbi.1000881VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity.Brian Y ChenBarry HonigMany algorithms that compare protein structures can reveal similarities that suggest related biological functions, even at great evolutionary distances. Proteins with related function often exhibit differences in binding specificity, but few algorithms identify structural variations that effect specificity. To address this problem, we describe the Volumetric Analysis of Surface Properties (VASP), a novel volumetric analysis tool for the comparison of binding sites in aligned protein structures. VASP uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods. Our approach, inspired by techniques from constructive solid geometry, enables the isolation of volumetrically conserved and variable regions within three dimensionally superposed volumes. We applied VASP to compute a comparative volumetric analysis of the ligand binding sites formed by members of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains and the serine proteases. Within both families, VASP isolated individual amino acids that create structural differences between ligand binding cavities that are known to influence differences in binding specificity. Also, VASP isolated cavity subregions that differ between ligand binding cavities which are essential for differences in binding specificity. As such, VASP should prove a valuable tool in the study of protein-ligand binding specificity.http://europepmc.org/articles/PMC2930297?pdf=render |
| spellingShingle | Brian Y Chen Barry Honig VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. PLoS Computational Biology |
| title | VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. |
| title_full | VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. |
| title_fullStr | VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. |
| title_full_unstemmed | VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. |
| title_short | VASP: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. |
| title_sort | vasp a volumetric analysis of surface properties yields insights into protein ligand binding specificity |
| url | http://europepmc.org/articles/PMC2930297?pdf=render |
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