Fuzziness and frustration in the energy landscape of protein folding, function, and assembly

S Gianni, MI Freiberger, P Jemth… - Accounts of chemical …, 2021 - ACS Publications
Conspectus Are all protein interactions fully optimized? Do suboptimal interactions
compromise specificity? What is the functional impact of frustration? Why does evolution not …

Consensus protein design

BT Porebski, AM Buckle - Protein Engineering, Design and …, 2016 - academic.oup.com
A popular and successful strategy in semi-rational design of protein stability is the use of
evolutionary information encapsulated in homologous protein sequences. Consensus …

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

RG Parra, NP Schafer, LG Radusky… - Nucleic acids …, 2016 - academic.oup.com
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at
localizing and quantifying the energetic frustration present in protein molecules. Frustration …

Third generation antibody discovery methods: in silico rational design

P Sormanni, FA Aprile, M Vendruscolo - Chemical Society Reviews, 2018 - pubs.rsc.org
Owing to their outstanding performances in molecular recognition, antibodies are
extensively used in research and applications in molecular biology, biotechnology and …

[HTML][HTML] Towards a structural biology of the hydrophobic effect in protein folding

C Camilloni, D Bonetti, A Morrone, R Giri… - Scientific reports, 2016 - nature.com
The hydrophobic effect is a major driving force in protein folding. A complete understanding
of this effect requires the description of the conformational states of water and protein …

Frustration, function and folding

DU Ferreiro, EA Komives, PG Wolynes - Current opinion in structural …, 2018 - Elsevier
Natural protein molecules are exceptional polymers. Encoded in apparently random strings
of amino-acids, these objects perform clear physical tasks that are rare to find by simple …

Automated optimisation of solubility and conformational stability of antibodies and proteins

A Rosace, A Bennett, M Oeller, MM Mortensen… - Nature …, 2023 - nature.com
Biologics, such as antibodies and enzymes, are crucial in research, biotechnology,
diagnostics, and therapeutics. Often, biologics with suitable functionality are discovered, but …

Energy landscapes of functional proteins are inherently risky

A Gershenson, LM Gierasch, A Pastore… - Nature chemical …, 2014 - nature.com
Evolutionary pressure for protein function leads to unavoidable sampling of conformational
states that are at risk of misfolding and aggregation. The resulting tension between …

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics

GH Zerze, CM Miller, D Granata… - Journal of chemical theory …, 2015 - ACS Publications
Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under
physiological conditions, make up a large fraction of eukaryotic proteins. Molecular …

Deciphering the dark proteome of Chikungunya virus

A Singh, A Kumar, R Yadav, VN Uversky, R Giri - Scientific reports, 2018 - nature.com
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus. The outbreak of CHIKV
infection has been seen in many tropical and subtropical regions of the biosphere. Current …