Protein Structure Comparison by Alignment of Distance Matrices
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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The templates were pairwise structurally aligned according to DALILite, using HIF-2α as a reference, and sequence alignments were obtained by CLUSTALW and confirmed using the Align-2D command within MODELLER.
“The templates were pairwise structurally aligned according to DALILite (41,42), using HIF-2 α as a reference. The sequence alignments were obtained by CLUSTALW (43), and the result was confirmed using the Align-2D command within the MODELLER program (37-39).”
From Structural and Functional Characterization of the Aryl Hydrocarbon Receptor Ligand Binding Domain by Homology Modeling and Mutational Analysis (2007) · cites this paper as [41]
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“Since DALI only reports those alignments of significant Z -score and 17 086/39 800 pairs have DALI outputs, we take averages for all four methods over these 17 086 structural pairs in the lower part of Table 1.”
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Protein Structures Forming the Shell of Primitive Bacterial Organelles
Kerfeld, C. A., Sawaya, M. R., Tanaka, S., Nguyen, C. V., Phillips, M. L., Beeby, M., & Yeates, T. O. (2005) · Science · doi:10.1126/science.1113397 · Cited by 443 · see citing works
Structure and E3‐ligase activity of the Ring–Ring complex of Polycomb proteins Bmi1 and Ring1b
Buchwald, G., van der Stoop, P. P. M., Weichenrieder, O., Anastassis Perrakis, A., van Lohuizen, M., & Sixma, T. K. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601144 · Cited by 438 · see citing works
“Comparison of the individual Bmi1 and Ring1b structures to the PDB using the DALI server (Holm and Sander, 1993) Figure 2 Specific E2 requirement for histone H2A ubiquitination by the Ring1b159/Bmi1109 complex.”
MethodInfluentialLim, D., & Strynadka, N. C. J. (2002) · Nature Structural Biology · doi:10.1038/nsb858 · Cited by 442 · see citing works
The crystal structure of chloroperoxidase: a heme peroxidase–cytochrome P450 functional hybrid
Sundaramoorthy, M., Terner, J., & Poulos, T. L. (1995) · Structure · doi:10.1016/s0969-2126(01)00274-x · Cited by 440 · see citing works
A method for simultaneous alignment of multiple protein structures
Shatsky, M., Nussinov, R., & Wolfson, H. J. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10628 · Cited by 438 · see citing works
“Holm & Sander 28 show an alignment of the Rop protein (1rop) with cytochrome b56 (256b).”
BackgroundBorgstahl, G. E. O., Williams, D. R., & Getzoff, E. D. (1995) · Biochemistry · doi:10.1021/bi00019a004 · Cited by 437 · see citing works
ECOD: an evolutionary classification of protein domains
Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B.-H., & Grishin, N. V. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003926 · Cited by 426 · see citing works
“In order to extend distant evolutionary relationships beyond the SCOP superfamily level in ECOD, we apply state of the art homology-inference algorithms both developed in our group [19,20] as well as by others [21,22], manually analyze and verify the suggested homologous links, and incorporate findings from literature.”
MethodInfluentialCrystal structure of RecBCD enzyme reveals a machine for processing DNA breaks
Singleton, M. R., Dillingham, M. S., Gaudier, M., Kowalczykowski, S. C., & Wigley, D. B. (2004) · Nature · doi:10.1038/nature02988 · Cited by 424 · see citing works
“The fold of this domain has not previously been observed, according to the DALI serve”
MethodA New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
Schmitt, S., Kühn, D., & Klebe, G. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00811-2 · Cited by 423 · see citing works
Dali/FSSP classification of three-dimensional protein folds
Holm, L., & Sander, C. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.231 · Cited by 421 · see citing works
Self-citationSintchak, M. D., Fleming, M. A., Futer, O., Raybuck, S. A., Chambers, S. P., Caron, P. R., Murcko, M. A., & Wilson, K. P. (1996) · Cell · doi:10.1016/s0092-8674(00)81275-1 · Cited by 427 · see citing works
Structural basis for Ca2+-induced activation of human PAD4
Arita, K., Hashimoto, H., Shimizu, T., Nakashima, K., Yamada, M., & Sato, M. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb799 · Cited by 425 · see citing works
Klein, D. J., Moore, P. B., & Steitz, T. A. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.03.076 · Cited by 413 · see citing works
Structure of the Escherichia coli Fumarate Reductase Respiratory Complex
Iverson, T. M., Luna-Chavez, C., Cecchini, G., & Rees, D. C. (1999) · Science · doi:10.1126/science.284.5422.1961 · Cited by 416 · see citing works
Recent improvements to the PROSITE database
Hulo, N. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh044 · Cited by 415 · see citing works
“Several of our profiles have been built by a mixture of classical alignment and structural alignment with the help of T-Coffee or by pure structural alignment provided by the DALI algorithm (11).”
MethodNickel Superoxide Dismutase Structure and Mechanism
Barondeau, D. P., Kassmann, C. J., Bruns, C. K., Tainer, J. A., & Getzoff, E. D. (2004) · Biochemistry · doi:10.1021/bi0496081 · Cited by 415 · see citing works
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer
Johansson, M. U., Zoete, V., Michielin, O. A., & Guex, N. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-173 · Cited by 404 · see citing works
Metabolic Enzymes of Mycobacteria Linked to Antioxidant Defense by a Thioredoxin-Like Protein
Bryk, R., Lima, C. D., Erdjument‐Bromage, H., Tempst, P., & Nathan, C. (2002) · Science · doi:10.1126/science.1067798 · Cited by 400 · see citing works
- Authors
- Holm, L., & Sander, C.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1993-09
- Volume
- 233
- Issue
- 1
- Pages
- 123-138
- ISSN
- 0022-2836 (ISSN-L)
- 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
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › 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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