Design of structurally distinct proteins using strategies inspired by evolution

TM Jacobs, B Williams, T Williams, X Xu, A Eletsky… - Science, 2016 - science.org
Natural recombination combines pieces of preexisting proteins to create new tertiary
structures and functions. We describe a computational protocol, called SEWING, which is …

Context-dependent design of induced-fit enzymes using deep learning generates well-expressed, thermally stable and active enzymes

L Zimmerman, N Alon, I Levin… - Proceedings of the …, 2024 - National Acad Sciences
The potential of engineered enzymes in industrial applications is often limited by their
expression levels, thermal stability, and catalytic diversity. De novo enzyme design faces …

Protein salvage and repurposing in evolution: Phospholipase D toxins are stabilized by a remodeled scrap of a membrane association domain

MHJ Cordes, AK Sundman, HC Fox… - Protein …, 2023 - Wiley Online Library
The glycerophosphodiester phosphodiesterase (GDPD)‐like SMaseD/PLD domain family,
which includes phospholipase D (PLD) toxins in recluse spiders and actinobacteria, evolved …

A network biology approach to understanding the importance of chameleon proteins in human physiology and pathology

G Bahramali, B Goliaei, Z Minuchehr, SA Marashi - Amino acids, 2017 - Springer
Chameleon proteins are proteins which include sequences that can adopt α-helix–β-strand
(HE-chameleon) or α-helix–coil (HC-chameleon) or β-strand–coil (CE-chameleon) …

Classification of proteins: available structural space for molecular modeling

A Andreeva - Homology Modeling: Methods and Protocols, 2012 - Springer
The wealth of available protein structural data provides unprecedented opportunity to study
and better understand the underlying principles of protein folding and protein structure …

A role for indels in the evolution of Cro protein folds

KL Stewart, MR Nelson, KV Eaton… - Proteins: Structure …, 2013 - Wiley Online Library
Insertions and deletions in protein sequences, or indels, can disrupt structure and may result
in changes in protein folds during evolution or in association with alternative splicing. Pfl 6 …

Analysis of conformational variation in macromolecular structural models

SK Srivastava, S Gayathri, BA Manjasetty, B Gopal - PLoS One, 2012 - journals.plos.org
Experimental conditions or the presence of interacting components can lead to variations in
the structural models of macromolecules. However, the role of these factors in …

[图书][B] Single-molecule studies of prion protein folding and misfolding

H Yu - 2013 - search.proquest.com
Protein folding involves a stochastic search through the configurational energy landscape
towards the native structure. Although most proteins have evolved to fold efficiently into a …