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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Gruene, T., Brzeski, J., Eberharter, A., Clapier, C. R., Corona, D. F. V., Becker, P. B., & Müller, C. W. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00273-9 · Cited by 300
Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2.
Mattevi, A., Vanoni, M. A., Todone, F., et al. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.15.7496 · Cited by 283
CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs
Kitadokoro, K., Bordo, D., Galli, G., Petracca, R., Falugi, F., Abrignani, S., Grandi, G., & Bolognesi, M. (2001) · The EMBO Journal · doi:10.1093/emboj/20.1.12 · Cited by 301
Three-Dimensional Structure and Stability of the KH Domain: Molecular Insights into the Fragile X Syndrome
Musco, G., Stier, G., Joseph, C., Morelli, M. A. C., Nilges, M., Gibson, T. J., & Pastore, A. (1996) · Cell · doi:10.1016/s0092-8674(00)81100-9 · Cited by 283
“Efficient compuStructure database superpositions were performed with the pro- tation of three-dimensional protein structure in solution from nuclear gram DALI (Holm and Sander, 1993). magnetic resonance using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA.”
Method
Crystal Structure of the N-Terminal Domain of Sialoadhesin in Complex with 3′ Sialyllactose at 1.85 Å Resolution
May, A. P., Robinson, R. C., Vinson, M. C., Crocker, P. R., & Jones, E. Y. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80071-4 · Cited by 283
COMPASS: A Tool for Comparison of Multiple Protein Alignments with Assessment of Statistical Significance
Sadreyev, R. I., & Grishin, N. V. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01371-2 · Cited by 279
“In both cases, we based our evaluation on the comparison of the produced alignments to the structural alignments from the FSSP database(43,44) generated by the DALI method.(45) The results of the evaluation were compared to the results for the corresponding sequence–profile comparisons by PSI-BLAST, and to the results…”
Result
X‐ray crystal structure of rabbit N‐acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily
Ünligil, U. M., Zhou, S., Yuwaraj, S., Sarkar, M., Schachter, H., & Rini, J. M. (2000) · The EMBO Journal · doi:10.1093/emboj/19.20.5269 · Cited by 276
Crystal structure of reovirus attachment protein σ1 reveals evolutionary relationship to adenovirus fiber
Chappell, J. D., Prota, A. E., Dermody, T. S., & Stehle, T. (2002) · The EMBO Journal · doi:10.1093/emboj/21.1.1 · Cited by 278
RNA Polymerase: Structural Similarities Between Bacterial RNA Polymerase and Eukaryotic RNA Polymerase II
Ebright, R. H. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4309 · Cited by 277
The Structure of the CYLD USP Domain Explains Its Specificity for Lys63-Linked Polyubiquitin and Reveals a B Box Module
Komander, D., Lord, C. J., Scheel, H., Swift, S., Hofmann, K., Ashworth, A., & Barford, D. (2008) · Molecular Cell · doi:10.1016/j.molcel.2007.12.018 · Cited by 285
Structure of the Alzheimer's Disease Amyloid Precursor Protein Copper Binding Domain
Barnham, K. J., McKinstry, W. J., Multhaup, G., Galatis, D., Morton, C. J., Curtain, C. C., Williamson, N. A., White, A. R., Hinds, M. G., Norton, R. S., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300629200 · Cited by 274
Crystal structures of the bovine β4galactosyltransferase catalytic domain and its complex with uridine diphosphogalactose
Gastinel, L. N., Cambillau, C., & Bourne, Y. (1999) · The EMBO Journal · doi:10.1093/emboj/18.13.3546 · Cited by 272
“A structural homology search using DALI databases showed that the overall fold of β4Gal-T1 is different from any fold previously determined (Holm and Sander, 1983), indicating that no structural homology was apparent with the bacteriophage T4 DNA modifying enzyme β-glucosyltransferase structure…”
Method
Structure of a water soluble fragment of the ‘Rieske’ iron–sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 å resolution
Iwata, S., Saynovits, M., Link, T. A., et al. (1996) · Structure · doi:10.1016/s0969-2126(96)00062-7 · Cited by 273
Full‐length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2
Shin, D. S., Pellegrini, L., Daniels, D. S., Yelent, B., Craig, L., Bates, D. L., Yu, D. S., Shivji, M. K. K., Hitomi, C., Arvai, A. S., et al. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg429 · Cited by 270
Cocrystal Structure of a tRNA Ψ55 Pseudouridine Synthase
Hoang, C., & Ferré-D’Amaré, A. R. (2001) · Cell · doi:10.1016/s0092-8674(01)00618-3 · Cited by 287
Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases
Pellicena, P., Karow, D. S., Boon, E. M., Marletta, M. A., & Kuriyan, J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405188101 · Cited by 271
The Protein Model Portal—a comprehensive resource for protein structure and model information
Haas, J., Roth, S., Arnold, K., Kiefer, F., Schmidt, T., Bordoli, L., & Schwede, T. F. (2013) · Database · doi:10.1093/database/bat031 · Cited by 268
“To achieve this, the Euclidean distance from the mean dm,ij dij is weighted with an exponential term analogous to the Holm/Sander approach (36).”
Method
The death domain superfamily: a tale of two interfaces?
Weber, C. H., & Vincenz, C. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01905-3 · Cited by 271
Iron–sulfur protein folds, iron–sulfur chemistry, and evolution
Meyer, J. (2007) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-007-0318-7 · Cited by 277
Solution structure of cyanovirin-N, a potent HIV-inactivating protein
Bewley, C. A., Gustafson, K. R., Boyd, M. R., Covell, D. G., Bax, A., Clore, G. M., & Gronenborn, A. M. (1998) · Nature Structural Biology · doi:10.1038/828 · Cited by 266
“Similarly, a search of the Brookhaven protein structure database using the program DAL”
Method
Structure of the multimodular endonuclease FokI bound to DNA
Wah, D. A., Hirsch, J. A., Dorner, L. F., Schildkraut, I., & Aggarwal, A. K. (1997) · Nature · doi:10.1038/40446 · Cited by 266
Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-Å resolution
van Aalten, D. M. F., Synstad, B., Brurberg, M. B., Hough, E., Riise, B. W., Eijsink, V. G. H., & Wierenga, R. K. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.11.5842 · Cited by 266

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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