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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Background
The crystal structure of pneumococcal surface antigen PsaA reveals a metal-binding site and a novel structure for a putative ABC-type binding protein
Lawrence, M. C., Pilling, P. A., Epa, V. C., Berry, A. M., Ogunniyi, A. D., & Paton, J. C. (1998) · Structure · doi:10.1016/s0969-2126(98)00153-1 · Cited by 224
“The structure of PsaA was compared to those in the Brookhaven Protein Data Bank (PDB) by submitting the Cα coordinates of PsaA to the DALI server [15].”
Method
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
Gerstein, M., & Levitt, M. (1998) · Protein Science · doi:10.1002/pro.5560070226 · Cited by 221
“…& Matthews, 1980; Satow et al., 1987; Artymiuk et al., 1989; Taylor & Orengo, 1989; Sali & Blundell, 1990; Vriend et al., 1991; Russell & Barton, 1992; Grindley et al., 1993; Holm & Sander, 1993a; Godzik & Skolnick, 1994; Feng & Sippl, 1996; Falicov & Cohen, 1996; Gibrat et al., 1996; Cohen, 1997).”
BackgroundMethodInfluential
Structure of the Regulatory Hyaluronan Binding Domain in the Inflammatory Leukocyte Homing Receptor CD44
Teriete, P., Banerji, S., Noble, M. E. M., Blundell, C. D., Wright, A. J., Pickford, A. R., Lowe, E. D., Mahoney, D. J., Tammi, M., Kahmann, J. D., et al. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00080-2 · Cited by 222
Structure of the Reovirus Membrane-Penetration Protein, μ1, in a Complex with Its Protector Protein, σ3
Liemann, S., Chandran, K., Baker, T. S., Nibert, M. L., & Harrison, S. C. (2002) · Cell · doi:10.1016/s0092-8674(02)00612-8 · Cited by 226
“Comparison, using the DALI algorithm (Holm and Sander, 1993), of domains I–III with all threedimensional protein structures in the Protein Data Bank reveals no closely related protein fold.”
Protein function annotation by homology-based inference
Loewenstein, Y., Raimondo, D., Redfern, O., Watson, J., Frishman, D., Michal Linial, B., Orengo, C. A., Thornton, J. M., & Tramontano, A. L. (2009) · Genome biology · doi:10.1186/gb-2009-10-2-207 · Cited by 221
“Although not directly coupled to a curated domainfamily resource such as CATH and SCOP, other global structure-comparison methods (for example, DALI [33], MSDFold [34], VAST [35], CE [36], STRUCTAL [37] and FATCAT [38]) can identify structural neighbors in the Protein Data Bank (PDB) [39] (see Box 1), which may share…”
Method
DNA bending and a flip‐out mechanism for base excision by the helix–hairpin–helix DNA glycosylase, Escherichia coli AlkA
Hollis, T., Ichikawa, Y., & Ellenberger, T. (2000) · The EMBO Journal · doi:10.1093/emboj/19.4.758 · Cited by 222
“The sequences of AlkA, MutY and Endo III are aligned based on the best superposition of Cα atoms in the crystal structures, as determined by the program DALI (Holm and Sander, 1993).”
Method
Crystal structure of the surfactin synthetase‐activating enzyme Sfp: a prototype of the 4′‐phosphopantetheinyl transferase superfamily
Reuter, K., Mofid, M. R., Marahiel, M. A., & Ficner, R. (1999) · The EMBO Journal · doi:10.1093/emboj/18.23.6823 · Cited by 221
“program DALI (Holm and Sander, 1993) did not reveal a protein structure with significant similarity to Sfp.”
BackgroundMethod
Two independent routes of de novo vitamin B6 biosynthesis: not that different after all
Fitzpatrick, T. B., Amrhein, N., Kappes, B., Macheroux, P., Tews, I., & Raschle, T. (2007) · Biochemical Journal · doi:10.1042/bj20070765 · Cited by 221
Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage φ29 connector particle 1 1Edited by R. Huber
Guasch, A., Pous, J., Ibarra, B., Gomis‐Rüth, F. X., Valpuesta, J., de Sousa, N. C., Carrascosa, J. L., & Coll, M. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5278 · Cited by 223
Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites
Parris, K. D., Lin, L., Tam, A., Mathew, R. S., Hixon, J., Stahl, M., Fritz, C., Seehra, J. S., & Somers, W. S. (2000) · Structure · doi:10.1016/s0969-2126(00)00178-7 · Cited by 217
AIF promotes chromatinolysis and caspase‐independent programmed necrosis by interacting with histone H2AX
Artus, C., Boujrad, H., Bouharrour, A., Brunelle-Navas, M.-N., Hoos, S., Yuste, V. J., Lenormand, P., Rousselle, J.-C., Namane, A., England, P., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.43 · Cited by 230
“H2AX structure was modelled from NCP with DALI (Holm and Sander, 1993).”
Method
Activity of wheat α‐amylase inhibitors towards bruchid α‐amylases and structural explanation of observed specificities
Franco, O. L., Rigden, D. J., Melo, F. R., Bloch, C., Silva, C. P., & Grossi‐de‐Sá, M. F. (2000) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.2000.01199.x · Cited by 221
The folding catalyst protein disulfide isomerase is constructed of active and inactive thioredoxin modules
Kemmink, J., Darby, N. J., Dijkstra, K., et al. (1997) · Current Biology · doi:10.1016/s0960-9822(06)00119-9 · Cited by 220
The Structure of the Fusion Glycoprotein of Newcastle Disease Virus Suggests a Novel Paradigm for the Molecular Mechanism of Membrane Fusion
Chen, L., Gorman, J. J., McKimm‐Breschkin, J. L., Lawrence, L. J., Tulloch, P. A., Smith, B. J., Colman, P. M., & Lawrence, M. C. (2001) · Structure · doi:10.1016/s0969-2126(01)00581-0 · Cited by 222
Crystal Structure of a Flp Recombinase–Holliday Junction Complex Assembly of an Active Oligomer by Helix Swapping
Chen, Y. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)00086-1 · Cited by 219
“The N-terminal domain, residues 2–107, is structurally unrelated to the N-terminal domains of other family members, and we found no significant structural homologs for it in the protein data bank using the Dali webserver (Holm and Sander, 1993).”
Background
Placement of the Structural Proteins in Sindbis Virus
Zhang, W., Mukhopadhyay, S., Pletnev, S. V., Baker, T. S., Kuhn, R. J., & Rossmann, M. G. (2002) · Journal of Virology · doi:10.1128/jvi.76.22.11645-11658.2002 · Cited by 218
“A rough scale of similarity can be established by measuring the number and percentage of C atoms that can be sequentially aligned in three dimensions (22, 31, 56).”
Background
Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding
Daniels, D. S., Mol, C. D., Arvai, A. S., Kanugula, S., Pegg, A. E., & Tainer, J. A. (2000) · The EMBO Journal · doi:10.1093/emboj/19.7.1719 · Cited by 219
“Structurally implicated DNA-binding mode To elucidate the manner in which AGT binds DNA, we used the DALI structural comparison algorithm (Holm and Sander, 1993) to search for DNA-binding proteins with homology to AGT.”
Method
A Conserved HEAT Domain within eIF4G Directs Assembly of the Translation Initiation Machinery
Marcotrigiano, J., Lomakin, I. B., Sonenberg, N., Pestova, T. V., Hellen, C. U. T., & Burley, S. K. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00167-8 · Cited by 223
Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex
Chowdhury, S., Carter, J. J., Rollins, M. F., Golden, S. M., Jackson, R. N., Hoffmann, C., Nosaka, L., Bondy‐Denomy, J., Maxwell, K. L., Davidson, A. R., et al. (2017) · Cell · doi:10.1016/j.cell.2017.03.012 · Cited by 216
“(C) The Cas8f structurewas used to perform structural homology search usingDali (Holm and Sander, 1993).”
BackgroundMethodInfluential
Crystal structure and biochemical analyses reveal Beclin 1 as a novel membrane binding protein
Huang, W., Choi, W.-Y., Hu, W., Mi, N., Guo, Q., Ma, M., Liu, M., Tian, Y., Lu, P., Wang, F., et al. (2012) · Cell Research · doi:10.1038/cr.2012.24 · Cited by 223
An NMR approach to structural proteomics
Yee, A. A., Chang, X., Pineda‐Lucena, A., Wu, B., Semesi, A., Le, B., Ramelot, T. A., Lee, G., Bhattacharyya, S., Gutierrez, P., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.042684599 · Cited by 217
Paired Receptor Specificity Explained by Structures of Signal Regulatory Proteins Alone and Complexed with CD47
Hatherley, D., Graham, S. C., Turner, J., Harlos, K., Stuart, D. I., & Barclay, A. N. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.05.026 · Cited by 216
Crystal Structure of Long-Chain Alkane Monooxygenase (LadA) in Complex with Coenzyme FMN: Unveiling the Long-Chain Alkane Hydroxylase
Li, L., Liu, X., Yang, W., Feng, X., Wang, W., Feng, L., Bartlam, M. G., Wang, L., & Rao, Z. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.11.069 · Cited by 217
Structure of the catalytic domain of the hepatitis C virus NS2-3 protease
Lorenz, I. C., Marcotrigiano, J., Dentzer, T. G., et al. (2006) · Nature · doi:10.1038/nature04975 · Cited by 215

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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