Online citations, reference lists, and bibliographies.
← Back to Search

Optimal Protein Structure Alignments By Multiple Linkage Clustering: Application To Distantly Related Proteins.

N. Boutonnet, M. Rooman, M. Ochagavía, J. Richelle, S. Wodak
Published 1995 · Biology, Medicine

Cite This
Download PDF
Analyze on Scholarcy
Share
A fully automatic procedure for aligning two protein structures is presented. It uses as sole structural similarity measure the root mean square (r.m.s.) deviation of superimposed backbone atoms (N, C alpha, C and O) and is designed to yield optimal solutions with respect to this measure. In a first step, the procedure identifies protein segments with similar conformations in both proteins. In a second step, a novel multiple linkage clustering algorithm is used to identify segment combinations which yield optimal global structure alignments. Several structure alignments can usually be obtained for a given pair of proteins, which are exploited here to define automatically the common structural core of a protein family. Furthermore, an automatic analysis of the clustering trees is described which enables detection of rigid-body movements between structure elements. To illustrate the performance of our procedure, we apply it to families of distantly related proteins. One groups the three alpha + beta proteins ubiquitin, ferredoxin and the B1-domain of protein G. Their common structure motif consists of four beta-strands and the only alpha-helix, with one strand and the helix being displaced as a rigid body relative to the remaining three beta-strands. The other family consists of beta-proteins from the Greek key group, in particular actinoxanthin, the immunoglobulin variable domain and plastocyanin. Their consensus motif, composed of five beta-strands and a turn, is identified, mostly intact, in all Greek key proteins except the trypsins, and interestingly also in three other beta-protein families, the lipocalins, the neuraminidases and the lectins. This result provides new insights into the evolutionary relationships in the very diverse group of all beta-proteins.



This paper is referenced by
10.1186/1471-2105-9-257
SODa: An Mn/Fe superoxide dismutase prediction and design server
J. M. Kwasigroch (2007)
10.1002/prot.10587
Progressive combinatorial algorithm for multiple structural alignments: Application to distantly related proteins
M. Ochagavía (2004)
( N – 1 ) / 2 Pairwise Alignments Consistency – based Refinement Guide Tree Building Progressive Multiple Alignment Global Multiple Alignment
H. Zhou (2005)
10.1016/S1093-3263(00)00129-7
Comparing protein structures: a Gaussian-based approach to the three-dimensional structural similarity of proteins.
G. Maggiora (2001)
10.1021/ci050473v
In Silico Analysis of the Thermodynamic Stability Changes of Psychrophilic and Mesophilic alpha-Amylases upon Exhaustive Single-Site Mutations
D. Gilis (2006)
10.1134/S0006350912020030
Verification of the PREFAB alignment database
T. Astakhova (2012)
10.1186/1471-2105-12-472
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts
Xin Deng (2011)
10.1002/prot.21654
Assessing secondary structure assignment of protein structures by using pairwise sequence‐alignment benchmarks
W. Zhang (2008)
10.1093/nar/gkl514
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
J. Pei (2006)
10.1093/bioinformatics/18.4.637
Advanced pairwise structure alignments of proteins and analysis of conformational changes
M. Ochagavía (2002)
10.1371/journal.pone.0015388
Structural Relationships in the Lysozyme Superfamily: Significant Evidence for Glycoside Hydrolase Signature Motifs
Alexandre Wohlkönig (2010)
) / 2 Pairwise Alignments Consistency – based Refinement Guide Tree Building Progressive Multiple Alignment Global Multiple Alignment N Sequences
Hongyi Zhou (2005)
10.1016/S0958-1669(96)80127-3
Protein engineering
(1996)
A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment
Barics Ekim (2017)
10.1093/PROTEIN/13.11.745
ProSup: a refined tool for protein structure alignment.
P. Lackner (2000)
10.1093/bioinformatics/btq338
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
Yongchao Liu (2010)
10.1002/prot.10293
Consistency matrices: Quantified structure alignments for sets of related proteins
Ivo Van Walle (2003)
10.1093/nar/gkl344
Protemot: prediction of protein binding sites with automatically extracted geometrical templates
Darby Tien-Hao Chang (2006)
10.1002/JCCS.200300112
Stability and Unfolding Mechanism of the N‐terminal β‐Hairpin from [2Fe‐2S] Ferredoxin I by Molecular Dynamics Simulations
H. Liu (2003)
10.1186/1472-6807-6-17
Similar folds with different stabilization mechanisms: the cases of prion and doppel proteins
Stefano Colacino (2006)
10.1093/bioinformatics/14.6.516
A geometric algorithm to find small but highly similar 3D substructures in proteins
X. Pennec (1998)
alignment ProbCons : Probabilistic consistency-based multiple sequence data
Chuong B. Do (2005)
10.1021/bi800655u
X-ray structure of papaya chitinase reveals the substrate binding mode of glycosyl hydrolase family 19 chitinases.
J. Huet (2008)
10.1093/BIOINFORMATICS/BTG1086
Flexible structure alignment by chaining aligned fragment pairs allowing twists
Y. Ye (2003)
Improved computational methods of protein sequence alignment, model selection and tertiary structure prediction
Xin Deng (2013)
10.1038/NSB0597-357
Three-dimensional structure of staphylokinase, a plasminogen activator with therapeutic potential
A. Rabijns (1997)
10.1093/NAR/GKH340
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
R. Edgar (2004)
10.1093/BIOINFORMATICS/BTH493
SABmark- a benchmark for sequence alignment that covers the entire known fold space
I. V. Walle (2005)
10.1186/s12859-017-1703-z
PFASUM: a substitution matrix from Pfam structural alignments
Frank Keul (2017)
10.1002/(SICI)1097-0134(199707)28:3<360::AID-PROT6>3.0.CO;2-G
Refined solution structure of the anti‐mammal and anti‐insect LqqIII scorpion toxin: Comparison with other scorpion toxins
C. Landon (1997)
10.1109/BIBE.2004.1317374
An efficient mechanism for prediction of protein-ligand interactions based on analysis of protein tertiary substructures
Darby Tien-Hao Chang (2004)
automated method for model comparison MAMMOTH ( Matching molecular models obtained from theory ) : An
Angel R. Ortiz (2002)
See more
Semantic Scholar Logo Some data provided by SemanticScholar