Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them

J M  THORNTON; M W  MACARTHUR; I K  MCDONALD; D T  JONES; John Blayney Owen Mitchell; C L  NANDI; S L  PRICE; M J J M  ZVELEBIL

doi:10.1098/rsta.1993.0123

Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them

J M THORNTON, M W MACARTHUR, I K MCDONALD, D T JONES, John Blayney Owen Mitchell, C L NANDI, S L PRICE, M J J M ZVELEBIL

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Abstract

The rapid increase in the number of high-quality protein structures provides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes they form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of side chain/atom interactions to assess three different methods for modelling atomic interactions in proteins. We have also derived a new empirical solvation potential which aims to reproduce the hydrophobic effect. To conclude we address the problem of molecular recognition and consider what we can deduce about the interactions involved in the binding of peptides to proteins.

Original language	English
Pages (from-to)	113-129
Number of pages	17
Journal	Philosophical Transactions of the Royal Society of London. Series A, Physical Sciences and Engineering
Volume	345
Issue number	1674
DOIs	https://doi.org/10.1098/rsta.1993.0123
Publication status	Published - 15 Oct 1993

Keywords

DISTRIBUTED MULTIPOLE ANALYSIS
3-DIMENSIONAL STRUCTURE
SECONDARY STRUCTURE
CRYSTAL-STRUCTURES
GLOBULAR-PROTEINS
RECOGNITION
BINDING
PEPTIDE
MODELS
ENERGY

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THORNTON, J. M., MACARTHUR, M. W., MCDONALD, I. K., JONES, D. T., Mitchell, J. B. O., NANDI, C. L., PRICE, S. L., & ZVELEBIL, M. J. J. M. (1993). Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them. Philosophical Transactions of the Royal Society of London. Series A, Physical Sciences and Engineering, 345(1674), 113-129. https://doi.org/10.1098/rsta.1993.0123

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title = "Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them",

abstract = "The rapid increase in the number of high-quality protein structures provides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes they form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of side chain/atom interactions to assess three different methods for modelling atomic interactions in proteins. We have also derived a new empirical solvation potential which aims to reproduce the hydrophobic effect. To conclude we address the problem of molecular recognition and consider what we can deduce about the interactions involved in the binding of peptides to proteins.",

keywords = "DISTRIBUTED MULTIPOLE ANALYSIS, 3-DIMENSIONAL STRUCTURE, SECONDARY STRUCTURE, CRYSTAL-STRUCTURES, GLOBULAR-PROTEINS, RECOGNITION, BINDING, PEPTIDE, MODELS, ENERGY",

author = "THORNTON, {J M} and MACARTHUR, {M W} and MCDONALD, {I K} and JONES, {D T} and Mitchell, {John Blayney Owen} and NANDI, {C L} and PRICE, {S L} and ZVELEBIL, {M J J M}",

year = "1993",

month = oct,

day = "15",

doi = "10.1098/rsta.1993.0123",

language = "English",

volume = "345",

pages = "113--129",

journal = " Philosophical Transactions of the Royal Society of London. Series A, Physical Sciences and Engineering",

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THORNTON, JM, MACARTHUR, MW, MCDONALD, IK, JONES, DT, Mitchell, JBO, NANDI, CL, PRICE, SL & ZVELEBIL, MJJM 1993, 'Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them', Philosophical Transactions of the Royal Society of London. Series A, Physical Sciences and Engineering, vol. 345, no. 1674, pp. 113-129. https://doi.org/10.1098/rsta.1993.0123

Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them. / THORNTON, J M ; MACARTHUR, M W ; MCDONALD, I K et al.
In: Philosophical Transactions of the Royal Society of London. Series A, Physical Sciences and Engineering, Vol. 345, No. 1674, 15.10.1993, p. 113-129.

Research output: Contribution to journal › Article › peer-review

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T1 - Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them

AU - THORNTON, J M

AU - MACARTHUR, M W

AU - MCDONALD, I K

AU - JONES, D T

AU - Mitchell, John Blayney Owen

AU - NANDI, C L

AU - PRICE, S L

AU - ZVELEBIL, M J J M

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AB - The rapid increase in the number of high-quality protein structures provides an expanding knowledge resource about interactions involved in stabilizing protein three-dimensional structures and the complexes they form with other molecules. In this paper we first review the results of some recent analyses of protein structure, including restrictions on local conformation, and a study of the geometry of hydrogen bonds. Then we consider how such empirical data can be used as a test bed for energy calculations, by using the observed spatial distributions of side chain/atom interactions to assess three different methods for modelling atomic interactions in proteins. We have also derived a new empirical solvation potential which aims to reproduce the hydrophobic effect. To conclude we address the problem of molecular recognition and consider what we can deduce about the interactions involved in the binding of peptides to proteins.

KW - DISTRIBUTED MULTIPOLE ANALYSIS

KW - 3-DIMENSIONAL STRUCTURE

KW - SECONDARY STRUCTURE

KW - CRYSTAL-STRUCTURES

KW - GLOBULAR-PROTEINS

KW - RECOGNITION

KW - BINDING

KW - PEPTIDE

KW - MODELS

KW - ENERGY

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DO - 10.1098/rsta.1993.0123

M3 - Article

SN - 0962-8428

VL - 345

SP - 113

EP - 129

JO - Philosophical Transactions of the Royal Society of London. Series A, Physical Sciences and Engineering

JF - Philosophical Transactions of the Royal Society of London. Series A, Physical Sciences and Engineering

IS - 1674

ER -

Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them

Abstract

Keywords

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