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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Method
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Pedersen, J. T., & Moult, J. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1010 · Cited by 141
The CXCR3 Binding Chemokine IP-10/CXCL10: Structure and Receptor Interactions
Booth, V. K., Keizer, D. W., Kamphuis, M. B., Clark‐Lewis, I., & Sykes, B. D. (2002) · Biochemistry · doi:10.1021/bi026020q · Cited by 142
The Structure of Adrenodoxin Reductase of Mitochondrial P 450 Systems: Electron Transfer for Steroid Biosynthesis
Ziegler, G. A., Vonrhein, C., Hanukoglu, I., & Schulz, G. E. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2807 · Cited by 138
“Protein Data Bank accession numbers The coordinates and structure factors are deposited with the Protein Data Bank, Brookhaven, under accession number 1CJC.”
BackgroundMethodInfluential
The Nucleocapsid Protein of Coronavirus Infectious Bronchitis Virus: Crystal Structure of Its N-Terminal Domain and Multimerization Properties
Fan, H., Ooi, A., Tan, Y. W., et al. (2005) · Structure · doi:10.1016/j.str.2005.08.021 · Cited by 140
“Overall, a three-dimensional structural alignment between the SARS-CoV and IBV nucleocapsid N-terminal domains using the program DALI (Holm and Sander, 1993) shows that a total of 124 equivalent Ca atoms can be superimposed, with an rms deviation of 3.0 Å.”
MethodInfluential
Free methionine-( R )-sulfoxide reductase from Escherichia coli reveals a new GAF domain function
Lin, Z., Johnson, L. C., Weissbach, H., Brot, N., Lively, M. O., & Lowther, W. T. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703774104 · Cited by 139
Structure of the Sulfolobus solfataricus α-Glucosidase: Implications for Domain Conservation and Substrate Recognition in GH31
Ernst, H. A., Leggio, L. L., Willemoës, M., Leonard, G. A., Blum, P., & Larsen, S. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.056 · Cited by 143
Crystal structure of mammalian α1,6-fucosyltransferase, FUT8
Ihara, H., Ikeda, Y., Toma, Š., Wang, X., Suzuki, T., Gu, J., Miyoshi, E., Tomitake Tsukihara, A., Honke, K., Matsumoto, A., et al. (2006) · Glycobiology · doi:10.1093/glycob/cwl079 · Cited by 145
“In order to compare the fold of FUT8 with known structures, each part of the FUT8 structure was applied to database searching (DALI server) (Holm and Sander 1993).”
Method
Structure and Mechanism of Phosphoenolpyruvate Carboxykinase
Matte, A., Tari, L. W., Goldie, H., et al. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.13.8105 · Cited by 140
Structure of the Y14-Magoh Core of the Exon Junction Complex
Lau, C.-K., Diem, M. D., Dreyfuss, G., & Duyne, G. D. V. (2003) · Current Biology · doi:10.1016/s0960-9822(03)00328-2 · Cited by 143
Crystal structures of a novel, thermostable phytase in partially and fully calcium-loaded states.
Oh, B., Ha, N., Oh, B., Shin, S., Kim, H.-J., Oh, T.-K., Kim, Y., & Choi, K. Y. (2000) · Nature Structural Biology · doi:10.1038/72421 · Cited by 139
“A search for similar folds in the Protein Data Base using the program DAL”
Method
Siah ubiquitin ligase is structurally related to TRAF and modulates TNF-α signaling
Polekhina, G., House, C. M., Traficante, N., Mackay, J. P., Relaix, F., Sassoon, D. A., Parker, M. W., & Bowtell, D. D. L. (2001) · Nature Structural Biology · doi:10.1038/nsb743 · Cited by 137
“Siah SBD resembles the C-terminal domain of TRAF An automatic structural similarity search of the C-terminal domain of Siah, using DAL”
Method
DNA-repair protein hHR23a alters its protein structure upon binding proteasomal subunit S5a
Walters, K. J., Lech, P. J., Goh, A. M., Wang, Q., & Howley, P. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1634989100 · Cited by 141
Mutational studies on HslU and its docking mode with HslV
Song, H. K., Hartmann, C., Ramachandran, R., et al. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.250491797 · Cited by 139
Structure of the OmpA‐like domain of RmpM from Neisseria meningitidis
Grizot, S., & Buchanan, S. K. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2003.03903.x · Cited by 139
“A search performed by the program DALI (Holm and Sander, 1993) showed that the core of the protein formed by the b -sheet, a 2 and a 3 helices belongs to the family of the B. subtilis chorismate mutase-like fold (Chook et al ., 1994).”
Method
Trans‐activation of the DNA‐damage signalling protein kinase Chk2 by T‐loop exchange
Oliver, A. W., Paul, A., Boxall, K. J., Barrie, S. E., Aherne, G. W., Garrett, M. D., Mittnacht, S., & Pearl, L. H. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601209 · Cited by 136
“Comparison of the CHK2-KD structure with other known protein structures using DALI (Holm and Sander, 1993) Figure 1 Chk2 in the DNA damage signalling network.”
Influential
Optimum superimposition of protein structures: ambiguities and implications
Zu-Kang, F., & Sippl, M. J. (1996) · Folding and Design · doi:10.1016/s1359-0278(96)00021-1 · Cited by 137
“the fold classification based on structure/structure alignment of proteins [FSSP] database of structural similarities [10]).”
BackgroundMethodInfluential
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
Pandit, S. B., & Skolnick, J. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-531 · Cited by 138
“Some approaches compare the respective distance matrices of each protein structure, trying to minimize the intra-atomic distances for the set of aligned substructures [17-21]; this is the approach employed in the widely used DALI algorithm [18].”
Method
Novel β-Barrel Fold in the Nuclear Magnetic Resonance Structure of the Replicase Nonstructural Protein 1 from the Severe Acute Respiratory Syndrome Coronavirus
Almeida, M. S., Johnson, M. A., Herrmann, T., Geralt, M., & Kurt Wüthrich, A. (2007) · Journal of Virology · doi:10.1128/jvi.01939-06 · Cited by 136
“A search of the Protein Data Bank using the structure of nsp1 as input for the DALI server (26) did not indicate statistically significant structural similarity to any other protein described to date.”
Method
Mitochondrial Bol1 and Bol3 function as assembly factors for specific iron-sulfur proteins
Uzarska, M. A., Nasta, V., Weiler, B. D., Spantgar, F., Ciofi‐Baffoni, S., Saviello, M. R., Gonnelli, L., Mühlenhoff, U., Banci, L., & Lill, R. (2016) · eLife · doi:10.7554/elife.16673 · Cited by 138
“According to the DALI server (Holm and Sander, 1993), both BOLA1 and BOLA3 show the highest structural similarity to BolA-like proteins from Arabidopsis thaliana, Babesia bovis, and Mus musculus (Abendroth et al.”
Method
Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures.
Gerstein, M., & Levitt, M. (1996) · PubMed · Cited by 138
Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition
Ahn, H. J., Kim, H., Yoon, H., et al. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg269 · Cited by 137
Conjugated Bile Acid Hydrolase Is a Tetrameric N-Terminal Thiol Hydrolase with Specific Recognition of Its Cholyl but Not of Its Tauryl Product,
Rossocha, M., Schultz‐Heienbrok, R., von Moeller, H., Coleman, J. P., & Saenger, W. (2005) · Biochemistry · doi:10.1021/bi0473206 · Cited by 138
Quantifying the Similarities within Fold Space
Harrison, A., Pearl, F. M. G., Mott, R., Thornton, J. M., & Orengo, C. A. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00992-0 · Cited by 137

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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