Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

DA Capdevila, JJ Rondón, KA Edmonds… - Chemical …, 2024 - ACS Publications
Transition metals function as structural and catalytic cofactors for a large diversity of proteins
and enzymes that collectively comprise the metalloproteome. Metallostasis considers all …

The value of protein allostery in rational anticancer drug design: an update

R Nussinov, H Jang - Expert Opinion on Drug Discovery, 2024 - Taylor & Francis
Introduction Allosteric drugs are advantageous. However, they still face hurdles, including
identification of allosteric sites that will effectively alter the active site. Current strategies …

Integration of a randomized sequence scanning approach in AlphaFold2 and local frustration profiling of conformational states enable interpretable atomistic …

N Raisinghani, M Alshahrani, G Gupta… - Journal of Chemical …, 2024 - ACS Publications
Despite the success of AlphaFold methods in predicting single protein structures, these
methods showed intrinsic limitations in the characterization of multiple functional …

A contact‐based analysis of local energetic frustration dynamics identifies key residues enabling RfaH fold‐switch

J González‐Higueras, MI Freiberger… - Protein …, 2024 - Wiley Online Library
Fold‐switching enables metamorphic proteins to reversibly interconvert between two highly
dissimilar native states to regulate their protein functions. While about 100 proteins have …

Reassessing the exon–foldon correspondence using frustration analysis

EA Galpern, H Jaafari, C Bueno, PG Wolynes… - Proceedings of the …, 2024 - pnas.org
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept
of exons as potential protein folding modules across a set of 38 abundant and conserved …

Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with …

N Raisinghani, M Alshahrani, G Gupta, H Tian, S **ao… - bioRxiv, 2024 - biorxiv.org
The groundbreaking achievements of AlphaFold2 (AF2) approaches in protein structure
modeling marked a transformative era in structural biology. Despite the success of AF2 tools …

Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families

RG Parra, MI Freiberger, M Poley-Gil… - Nucleic Acids …, 2024 - academic.oup.com
According to the Principle of Minimal Frustration, folded proteins can only have a minimal
number of strong energetic conflicts in their native states. However, not all interactions are …

Evolution shapes interaction patterns for epistasis and specific protein binding in a two-component signaling system

Z Yan, J Wang - Communications Chemistry, 2024 - nature.com
The elegant design of protein sequence/structure/function relationships arises from the
interaction patterns between amino acid positions. A central question is how evolutionary …

Heterogeneous folding landscapes and predetermined breaking points within a protein family

S Pechmann - Protein Science, 2024 - Wiley Online Library
The accurate prediction of protein structures with artificial intelligence has been a
spectacular success. Yet, how proteins fold into their native structures inside the cell remains …

Insights From Protein Frustration Analysis of BRD4-Cereblon Degrader Ternary Complexes Show Separation of Strong from Weak Degraders

T Yang, E Mukhaleva, W Wei, D Weiss, N Ma… - RSC Medicinal …, 2025 - pubs.rsc.org
PROteolysis TArgeting Chimeras (PROTACs), also known as Ligand-Directed Degraders
(LDDs), are an innovative class of small molecules that leverage the ubiquitin-proteasome …