A Review of Methods for Protein Structure Comparison

As increasing numbers of structures are determined and compared, it has become apparent that there are extensive similarities in the chain fold (or topology) of many proteins. In recent years techniques have been developed which attempt to predict, or model, the structure of a protein from the amino acid sequence by utilising these common structural elements. In addition to identifying recurring topologies, structure comparisons have also revealed smaller structural fragments or motifs accross a wide range of proteins; for example, the βαβ and the β-hairpin motifs (see Thornton et al., in this Vol.). Characterising these motifs in terms of geometry, distance constraints and sequence composition can enhance protein structure prediction techniques by incorporating longer range interactions between secondary structures.

[1]  E. Padlan,et al.  Variability of three-dimensional structure in immunoglobulins. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[2]  S. Rackovsky,et al.  Differential geometry and protein folding , 1984 .

[3]  M. Perutz,et al.  The structure of haemoglobin. IX. A three-dimensional Fourier synthesis at 5.5 Å resolution: description of the structure , 1962, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[4]  S J Remington,et al.  Relation between hen egg white lysozyme and bacteriophage T4 lysozyme: evolutionary implications. , 1981, Journal of molecular biology.

[5]  S. Rackovsky,et al.  Differential Geometry and Polymer Conformation. 1. Comparison of Protein Conformations1a,b , 1978 .

[6]  S. Rackovsky.  Quantitative organization of the known protein x‐ray structures. I. Methods and short‐length‐scale results , 1990, Proteins.

[7]  M. Murthy,et al.  A fast method of comparing protein structures , 1984, FEBS letters.

[8]  M J Sippl,et al.  On the problem of comparing protein structures. Development and applications of a new method for the assessment of structural similarities of polypeptide conformations. , 1982, Journal of molecular biology.

[9]  Julian R. Ullmann,et al.  An Algorithm for Subgraph Isomorphism , 1976, J. ACM.

[10]  S J Remington,et al.  A systematic approach to the comparison of protein structures. , 1980, Journal of molecular biology.

[11]  F. Richards,et al.  Identification of structural motifs from protein coordinate data: Secondary structure and first‐level supersecondary structure * , 1988, Proteins.

[12]  P Argos,et al.  The taxonomy of protein structure. , 1977, Journal of molecular biology.

[13]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[14]  S. Rackovsky,et al.  Differential Geometry and Polymer Conformation. 2. Development of a Conformational Distance Function , 1980 .

[15]  C. Orengo,et al.  A rapid method of protein structure alignment. , 1990, Journal of theoretical biology.

[16]  G. Schulz,et al.  Gene duplication in glutathione reductase. , 1980, Journal of molecular biology.

[17]  T. Blundell,et al.  Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. , 1990, Journal of molecular biology.

[18]  P Willett,et al.  Use of techniques derived from graph theory to compare secondary structure motifs in proteins. , 1990, Journal of molecular biology.

[19]  I D Kuntz,et al.  An approach to the tertiary structure of globular proteins. , 1975, Journal of the American Chemical Society.

[20]  M G Rossmann,et al.  Comparison of super-secondary structures in proteins. , 1973, Journal of molecular biology.

[21]  D. Stuart,et al.  A method for the systematic comparison of the three‐dimensional structures of proteins and some results , 1984 .

[22]  A. D. McLachlan,et al.  Rapid comparison of protein structures , 1982 .

[23]  S J Remington,et al.  Atomic coordinates for T4 phage lysozyme. , 1977, Biochemical and biophysical research communications.

[24]  W R Taylor,et al.  A holistic approach to protein structure alignment. , 1989, Protein engineering.

[25]  P Argos,et al.  Exploring structural homology of proteins. , 1976, Journal of molecular biology.

[26]  P Argos,et al.  A comparison of the heme binding pocket in globins and cytochrome b5. , 1975, The Journal of biological chemistry.

[27]  M G Rossmann,et al.  Comparison of protein structures. , 1985, Methods in enzymology.

[28]  M. Zuker,et al.  The alignment of protein structures in three dimensions. , 1989, Bulletin of mathematical biology.

[29]  M. E. Karpen,et al.  Comparing short protein substructures by a method based on backbone torsion angles , 1989, Proteins.

[30]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.