Cited by 3,984Protein Structure and DynamicsEnzyme Structure and FunctionGenomics and Phylogenetic Studies

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Protein Structure Comparison by Alignment of Distance Matrices

Holm, Liisa, Sander, Chris·1993·Journal of Molecular Biology

DOI 10.1006/jmbi.1993.1489

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Abstract

With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known three-dimensional folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g. between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor.

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Cheever, M. L., Snyder, J. T., Gershburg, S., Siderovski, D. P., Harden, T. K., & Sondek, J. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1377 · Cited by 102
“The PDB was searched for structures with similarity to the DHEX domain using DAL”
Method
Dimeric structure of the cell shape protein MreC and its functional implications
van den Ent, F., Leaver, M., Bendezú, F. O., Errington, J., Boer, P. D., & Löwe, J. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05485.x · Cited by 101
“Three top scores of a structural similarity search with MreC among all known structures in the PDB (using DALI; Holm and Sander, 1993).”
Background
Crystal structure of human GM2-activator protein with a novel β-cup topology
Wright, C. S., Li, S., & Rastinejad, F. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4225 · Cited by 102
The 2.0 Å Crystal Structure of Cephalosporin Acylase
Kim, Y., Yoon, K.-H., Khang, Y., et al. (2000) · Structure · doi:10.1016/s0969-2126(00)00505-0 · Cited by 102
Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme
Changela, A., Ho, C. K., Martins, A., Shuman, S., & Mondragón, A. (2001) · The EMBO Journal · doi:10.1093/emboj/20.10.2575 · Cited by 100
Crystal Structure of the Borna Disease Virus Nucleoprotein
Rudolph, M. G., Kraus, I., Dickmanns, A., et al. (2003) · Structure · doi:10.1016/j.str.2003.08.011 · Cited by 101
“A search in the DALI database (Holm & Sander, 1993) with both, the whole model and the individual domains, did not reveal any significant homology to other known structures.”
Method
Novel Catalytic Mechanism of Glycoside Hydrolysis Based on the Structure of an NAD+/Mn2+-Dependent Phospho-α-Glucosidase from Bacillus subtilis
Rajan, S. S., Yang, X., Collart, F., et al. (2004) · Structure · doi:10.1016/j.str.2004.06.020 · Cited by 101
The SoxYZ Complex Carries Sulfur Cycle Intermediates on a Peptide Swinging Arm
Sauvé, V., Bruno, S., Berks, B. C., & Hemmings, A. M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m701602200 · Cited by 107
Objective comparison of protein structures: error-scaled difference distance matrices
Schneider, T. R. (2000) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444900003723 · Cited by 101
Similar modes of polypeptide recognition by export chaperones in flagellar biosynthesis and type III secretion
Evdokimov, A. G., Phan, J., Tropea, J. E., et al. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb982 · Cited by 101
“A search of the coordinates available from the Protein Data Bank with the program Dal”
Method
The First Structure of UDP-Glucose Dehydrogenase Reveals the Catalytic Residues Necessary for the Two-fold Oxidation,
Campbell, R. E., Mosimann, S. C., Rijn, I. V. D., et al. (2000) · Biochemistry · doi:10.1021/bi000181h · Cited by 101
Folding simulations and computer redesign of protein A three-helix bundle motifs
Olszewski, K. A., Koliński, A., & Skolnick, J. (1996) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199607)25:3 · Cited by 45
Recognition of ERK MAP kinase by PEA‐15 reveals a common docking site within the death domain and death effector domain
Hill, J. M., Vaidyanathan, H., Ramos, J. W., Ginsberg, M. H., & Werner, M. H. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf641 · Cited by 100
“melanogaster Pelle DD created from pairwise superpositions calculated in DALI (Holm and Sander, 1993).”
Method
A Structural Genomics Approach to the Study of Quorum Sensing
Lewis, H. A., Furlong, E. B., Laubert, B., et al. (2001) · Structure · doi:10.1016/s0969-2126(01)00613-x · Cited by 100
Crystal Structure of the Archaeal Holliday Junction Resolvase Hjc and Implications for DNA Recognition
Nishino, T., Komori, K., Tsuchiya, D., et al. (2001) · Structure · doi:10.1016/s0969-2126(01)00576-7 · Cited by 100
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes
Mosca, R., & Schneider, T. R. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn197 · Cited by 100
“The first group of computer programs includes DALI (5), CE (6) and MAMMOTH (7) for pairwise alignment and CEMC (8), SSM (9) and MAMMOTHMult (10) for multiple alignment.”
Method
The Three-Dimensional Structure of the Human NK Cell Receptor NKp44, a Triggering Partner in Natural Cytotoxicity
Cantoni, C., Ponassi, M., Biassoni, R., Conte, R., Spallarossa, A., Moretta, A., Moretta, L., Bolognesi, M., & Bordo, D. (2003) · Structure · doi:10.1016/s0969-2126(03)00095-9 · Cited by 100
Toward a Structural Understanding of the Dehydratase Mechanism
Allard, S. T. M., Beis, K., Giraud, M., et al. (2002) · Structure · doi:10.1016/s0969-2126(01)00694-3 · Cited by 100
The Active Conformation of Glutamate Synthase and its Binding to Ferredoxin
van den Heuvel, R. H. H., Svergun, D. I., Petoukhov, M. V., et al. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00522-9 · Cited by 100
Crystal structure of vesicular stomatitis virus matrix protein
Gaudier, M., Gaudin, Y., & Knossow, M. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf284 · Cited by 100
Co-crystal of Escherichia coli RNase HI with Mn2+ Ions Reveals Two Divalent Metals Bound in the Active Site
Goedken, E. R., & Marqusee, S. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m009626200 · Cited by 99
Solution structure of ThiS and implications for the evolutionary roots of ubiquitin.
Nicholson, L. K., Wang, C., Xi, J., & Begley, T. P. (2001) · Nature Structural Biology · doi:10.1038/83041 · Cited by 100
Comparative Analysis of Protein Structure Alignments
Mayr, G., Domingues, F. S., & Lackner, P. (2007) · BMC Structural Biology · doi:10.1186/1472-6807-7-50 · Cited by 99
“Several methods have been the focus of these analyses, in particular SSAP [30], STRUCTAL [31], DALI [13], LSQMAN [32], CE [12], SSM [29], ASH [27] and TM-align [28].”
Method
An Alternative Mechanism for Amidase Signature Enzymes
Labahn, J., Neumann, S., Büldt, G., Kula, M., & Granzin, J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00886-0 · Cited by 98

Authors: Holm, L., & Sander, C.
Affiliations: European Molecular Biology Laboratory (DE)
ORCID: Holm, Liisa
Sander, Chris
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1993-09
Volume: 233
Issue: 1
Pages: 123-138
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1993.1489
OpenAlex: W2022058405
Cited by: 3,984
References: 0
Citations by year: 2026: 23 · 2025: 31 · 2024: 22 · 2023: 22 · 2022: 28 · 2021: 27 · 2020: 53 · 2019: 50 · 2018: 45 · 2017: 42 · 2016: 53 · 2015: 65 · 2014: 73 · 2013: 106 · 2012: 98
FWCI: 15.32
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: protein structure comparison, Dali, Monte Carlo optimization, structural similarity, protein fold classification, structural core, colicin A, globin, lambda repressor, sequence gaps
MeSH terms: Actins, Algorithms, Amino Acid Sequence, Colicins, DNA-Binding Proteins, Globins, Heat-Shock Proteins, Hexokinase, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Muramidase, Software, Reproducibility of Results, Cluster Analysis, Sequence Alignment, Sequence Homology, Amino Acid, Protein Structure, Secondary, Protein Structure, Tertiary

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Protein Structure Comparison by Alignment of Distance Matrices

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