Fuzziness and frustration in the energy landscape of protein folding, function, and assembly
Conspectus Are all protein interactions fully optimized? Do suboptimal interactions
compromise specificity? What is the functional impact of frustration? Why does evolution not …
compromise specificity? What is the functional impact of frustration? Why does evolution not …
Consensus protein design
A popular and successful strategy in semi-rational design of protein stability is the use of
evolutionary information encapsulated in homologous protein sequences. Consensus …
evolutionary information encapsulated in homologous protein sequences. Consensus …
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at
localizing and quantifying the energetic frustration present in protein molecules. Frustration …
localizing and quantifying the energetic frustration present in protein molecules. Frustration …
Third generation antibody discovery methods: in silico rational design
Owing to their outstanding performances in molecular recognition, antibodies are
extensively used in research and applications in molecular biology, biotechnology and …
extensively used in research and applications in molecular biology, biotechnology and …
[HTML][HTML] Towards a structural biology of the hydrophobic effect in protein folding
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 …
of this effect requires the description of the conformational states of water and protein …
Frustration, function and folding
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 …
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 …
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 …
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
Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under
physiological conditions, make up a large fraction of eukaryotic proteins. Molecular …
physiological conditions, make up a large fraction of eukaryotic proteins. Molecular …
Deciphering the dark proteome of Chikungunya virus
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 …
infection has been seen in many tropical and subtropical regions of the biosphere. Current …