Basic units of protein structure, folding, and function

IN Berezovsky, E Guarnera, Z Zheng - Progress in biophysics and …, 2017 - Elsevier
Study of the hierarchy of domain structure with alternative sets of domains and analysis of
discontinuous domains, consisting of remote segments of the polypeptide chain, raised a …

Protein function machinery: from basic structural units to modulation of activity

IN Berezovsky, E Guarnera, Z Zheng… - Current opinion in …, 2017 - Elsevier
Highlights•Closed loops are universal basic units of globular proteins.•Enzymatic functions
are combined from elementary functional loops.•Structural dynamics is the cornerstone of …

Physics and evolution of thermophilic adaptation

IN Berezovsky, EI Shakhnovich - Proceedings of the …, 2005 - National Acad Sciences
Analysis of structures and sequences of several hyperthermostable proteins from various
sources reveals two major physical mechanisms of their thermostabilization. The first …

Closed loops of nearly standard size: common basic element of protein structure

IN Berezovsky, AY Grosberg, EN Trifonov - Febs Letters, 2000 - Wiley Online Library
By screening the crystal protein structure database for close Cα–Cα contacts, a size
distribution of the closed loops is generated. The distribution reveals a maximum at 27±5 …

[HTML][HTML] Living in trinity of extremes: genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation

A Amangeldina, ZW Tan, IN Berezovsky - Current Research in Structural …, 2024 - Elsevier
Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme
environmental conditions, it is possible to explore the genomic-proteomic compositional …

Conservation and diversity in allosteric fingerprints of proteins for evolutionary-inspired engineering and design

WV Tee, ZW Tan, E Guarnera, IN Berezovsky - Journal of Molecular Biology, 2022 - Elsevier
Hand-in-hand work of physics and evolution delivered protein universe with diversity of
forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an …

Van der Waals locks: loop-n-lock structure of globular proteins

IN Berezovsky, EN Trifonov - Journal of Molecular Biology, 2001 - Elsevier
In a globular protein the polypeptide chain returns to itself many times, making numerous
chain-to-chain contacts. The stability of these contacts is maintained primarily by van der …

Distinct stages of protein evolution as suggested by protein sequence analysis

EN Trifonov, A Kirzhner, VM Kirzhner… - Journal of molecular …, 2001 - Springer
Evolution of proteins encoded in nucleotide sequences began with the advent of the triplet
code. The chronological order of the appearance of amino acids on the evolution scene and …

Understanding the role of domain–domain linkers in the spatial orientation of domains in multi-domain proteins

RM Bhaskara, AG de Brevern… - Journal of Biomolecular …, 2013 - Taylor & Francis
Inter-domain linkers (IDLs)'bridge flanking domains and support inter-domain
communication in multi-domain proteins. Their sequence and conformational preferences …

ConDo: protein domain boundary prediction using coevolutionary information

SH Hong, K Joo, J Lee - Bioinformatics, 2019 - academic.oup.com
Motivation Domain boundary prediction is one of the most important problems in the study of
protein structure and function. Many sequence-based domain boundary prediction methods …