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Local sequence‐structure relationships in proteins
Author(s) -
Škrbić Tatjana,
Maritan Amos,
Giacometti Achille,
Banavar Jayanth R.
Publication year - 2021
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.4032
Subject(s) - loop modeling , sequence (biology) , protein data bank (rcsb pdb) , local structure , computational biology , protein structure , protein structure prediction , amino acid , similarity (geometry) , sequence alignment , peptide sequence , structural alignment , threading (protein sequence) , structural classification of proteins database , set (abstract data type) , biology , computer science , crystallography , chemistry , genetics , artificial intelligence , biochemistry , gene , programming language , image (mathematics)
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the putative native state folds from myriad possible conformations? In order to address these questions, we represent the local structure of each C α atom of a protein by just two angles, θ and μ, and we analyze a set of more than 4,000 protein structures from the PDB. We use a hierarchical clustering scheme to divide the 20 amino acids into six distinct groups based on their similarity to each other in fitting local structural space. We present the results of a detailed analysis of patterns of amino acid specificity in adopting local structural conformations and show that the sequence‐structure correlation is not very strong compared with a random assignment of sequence to structure. Yet, our analysis may be useful to determine an effective scoring rubric for quantifying the match of an amino acid to its putative local structure.