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
Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose
Charnock, S. J., Bolam, D. N., Nurizzo, D., Szabó, L., McKie, V. A., Gilbert, H. J., & Davies, G. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212516199 · Cited by 94
The 1.14 Å Crystal Structure of Yeast Cytosine Deaminase
Ireton, G. C., Black, M. E., & Stoddard, B. L. (2003) · Structure · doi:10.1016/s0969-2126(03)00153-9 · Cited by 93
The solution structure of VAT-N reveals a ‘missing link’ in the evolution of complex enzymes from a simple βαββ element
Coles, M. P., Diercks, T., Liermann, J., et al. (1999) · Current Biology · doi:10.1016/s0960-9822(00)80017-2 · Cited by 93
A unique fold of phospholipase C-β mediates dimerization and interaction with Gαq
Singer, A. U., Waldo, G. L., Harden, T. K., & Sondek, J. (2001) · Nature Structural Biology · doi:10.1038/nsb731 · Cited by 93
Alignment of 700 globin sequences: Extent of amino acid substitution and its correlation with variation in volume
Kapp, O. H., Moens, L. J., Vanfleteren, J., Trotman, C. N. A., Suzuki, T., & Vinogradov, S. N. (1995) · Protein Science · doi:10.1002/pro.5560041024 · Cited by 89
Crystal structure of a human aminoacyl-tRNA synthetase cytokine
Yang, X., Skene, R. J., McRee, D. E., & SCHIMMEL, P. R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242611799 · Cited by 93
Crystal Structure of Pseudouridine Synthase RluA: Indirect Sequence Readout through Protein-Induced RNA Structure
Hoang, C., Chen, J., Vizthum, C. A., et al. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.09.017 · Cited by 92
Local Protein Structures
Offmann, B., Tyagi, M., & de Brevern, A. (2007) · Current Bioinformatics · doi:10.2174/157489307781662105 · Cited by 96
“PB-ALIGN 18+ 17* 14 8 96.6 YAKUSA 17 19 14 8 95 CE 17 19 13 8 93 DALI 14 19 14 8 90 MATRAS 11 19 14 8 85 VAST 12 17 15 7 84 TOP 14 18 12 7 84 DEJAVU 14 19 9 4 75 TOPSCAN 15 12 9 7 70 TOPS 2 15 14 7 62 PRIDE 14 14 7 3 62 LOCK 0 14 11 8 54 SSM 5 13 10 5 54 Table 6.”
BackgroundInfluential
Streptococcus pneumoniae Endohexosaminidase D, Structural and Mechanistic Insight into Substrate-assisted Catalysis in Family 85 Glycoside Hydrolases
Abbott, D. W., Macauley, M. S., Vocadlo, D. J., et al. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m809663200 · Cited by 92
Kernels for Graphs
Kashima, H., Tsuda, K., & Inokuchi, A. (2004) · The MIT Press eBooks · doi:10.7551/mitpress/4057.003.0010 · Cited by 92
“In protein engineering, three dimensional structures of proteins are often represented as distance graphs (Holm and Sander, 1993).”
Background
Comparison of protein active site structures for functional annotation of proteins and drug design
Powers, R., Copeland, J. C., Germer, K., Mercier, K., Ramanathan, V., & Revesz, P. Z. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21092 · Cited by 91
“55 Again, this was based primarily on structural comparison using DALI 56 and VAST, 57 along with the presence of S -adenosyl- L -homocysteine.”
Method
Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns
Pires, D. E. V., de Melo-Minardi, R. C., dos Santos, M. A., da Silveira, C. H., Santoro, M. M., & Meira, W. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-s4-s12 · Cited by 92
“We can quote, for instance, the search for structural motifs [13-15] and functional residues (such as DNA [16] and metal [17] binding sites), the use of 3D templates [5] and the comparison of protein folds by structure alignments [18,19].”
Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8
Yamada, K., KUNISHIMA, N., Mayanagi, K., Ohnishi, T., Nishino, T., Iwasaki, H., Shinagawa, H., & Morikawa, K. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.4.1442 · Cited by 92
Crystal structure of a fungal elicitor secreted by Phytophthora cryptogea, a member of a novel class of plant necrotic proteins
Boissy, G., Fortelle, E. D. L., Kahn, R., et al. (1996) · Structure · doi:10.1016/s0969-2126(96)00150-5 · Cited by 92
Crystal structure of the amino-terminal domain of N-ethylmaleimide-sensitive fusion protein
May, A. P., Misura, K. M. S., Whiteheart, S. W., & Weis, W. I. (1999) · Nature Cell Biology · doi:10.1038/11097 · Cited by 92
“-cere---------TRTRHLKVSNCPNNSYALANVAAVSPNDFP--------NNIYII---IDNLFVFTTRHSN--DIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRA--(24-125) Sec18 -C.”
Influential
Four crystal structures of the 60 kDa flavoprotein monomer of the sulfite reductase indicate a disordered flavodoxin-like module 1 1Edited by R. Huber
Gruez, A., Pignol, D., Zeghouf, M., Covès, J., Fontecave, M., Ferrer, J.-L., & Fontecilla-Camps, J. C. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3748 · Cited by 91
Protein structure and evolutionary history determine sequence space topologyPreprint
Shakhnovich, B. E., Deeds, E. J., DeLisi, C., & Shakhnovich, E. I. (2005) · Genome Research · doi:10.1101/gr.3133605 · Cited by 89
“We use DALI29 to make all pairwise structural comparisons and we build structural neighborhoods as described in the text and in Fig1.”
MethodInfluential
Large-scale prediction of protein-protein interactions from structures
Hue, M., Riffle, M. E., Vert, J., et al. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-144 · Cited by 91
“A natural place to begin, when considering comparisons among protein structures, is with structural alignment algorithms such as CE [20], DALI [21] and MAMMOTH [22].”
Method
Structural and functional analysis of RNA and TAP binding to SF2/ASF
Tintaru, A., Hautbergue, G. M., Hounslow, A. M., et al. (2007) · EMBO Reports · doi:10.1038/sj.embor.7401031 · Cited by 91
“This is highlighted in supplementary Fig S1 online, in which the SF2/ASF fold is overlaid with structurally related proteins identified using the DALI server (Holm & Sander, 1993).”
Method
A common mechanism for ATP hydrolysis in ABC transporter and helicase superfamilies
Geourjon, C., Orelle, C., Steinfels, E., Blanchet, C., Deléage, G., Pietro, A. D., & Jault, J. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01907-7 · Cited by 96
Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N‐acetyl‐glucosamine
Blair, D. E., & van Aalten, D. M. F. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.06.013 · Cited by 91
“Searches for structural similarity with DALI [22] identified several ðb=aÞ8 proteins, including Tiny-TIM ([23], Fig.”
Background
Structure ofL-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family
Mattevi, A., Tedeschi, G., Bacchella, L., Coda, A., Negri, A. L., & Ronchi, S. (1999) · Structure · doi:10.1016/s0969-2126(99)80099-9 · Cited by 91
“All calculations relating to model validation, model analysis and structure comparisons were carried out with PROCHECK [52], DALI [24], the programs of the CCP4 suite [46] and of the ‘Uppsala Software Factory’ [53].”
BackgroundMethodInfluential
The Crystal Structure and Mutational Analysis of Human NUDT9
Shen, B. W., Perraud, A.-L., Scharenberg, A. M., et al. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00954-9 · Cited by 91
Molecular insights into the interaction of PYM with the Mago–Y14 core of the exon junction complex
Bono, F., Ebert, J., Unterholzner, L., et al. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400091 · Cited by 91
“The N-terminal region of PYM (3–35) folds with a three-stranded b-sheet and a contiguous b-hairpin, and does not resemble other known structures from database searches using the program DALI (Holm & Sander, 1993).”
Method
Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI
Roey, P. V., Meehan, L., Kowalski, J. C., Belfort, M., & Derbyshire, V. (2002) · Nature Structural Biology · doi:10.1038/nsb853 · Cited by 91
Analysis of the Structure, Substrate Specificity, and Mechanism of Squash Glycerol-3-Phosphate (1)-Acyltransferase
Turnbull, A. P., Rafferty, J. B., Sedelnikova, S. E., Slabas, A. R., Schierer, T. P., Kroon, J., Simon, J. W., Fawcett, T., Nishida, I., Murata, N., et al. (2001) · Structure · doi:10.1016/s0969-2126(01)00595-0 · Cited by 91
Crystal Structures of Escherichia coli ATP-Dependent Glucokinase and Its Complex with Glucose
Lunin, V. V., Li, Y., Schrag, J. D., et al. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.20.6915-6927.2004 · Cited by 91
Crystal Structure of GABA-Aminotransferase, a Target for Antiepileptic Drug Therapy
Storici, P., Capitani, G., Biase, D. D., et al. (1999) · Biochemistry · doi:10.1021/bi990478j · Cited by 91

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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