Tandon, Himani de Brevern, Alexandre G Srinivasan, Narayanaswamy
Published in
Structure (London, England : 1993)
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and struc...
Schoof, Michael Boone, Morgane Wang, Lan Lawrence, Rosalie Frost, Adam Walter, Peter
The integrated stress response (ISR) is activated by phosphorylation of the translation initiation factor eIF2 in response to various stress conditions. Phosphorylated eIF2 (eIF2-P) inhibits eIF2's nucleotide exchange factor eIF2B, a twofold symmetric heterodecamer assembled from subcomplexes. Here, we monitor and manipulate eIF2B assembly in vitro...
Fenton, Christopher A. Tang, Qingling Olson, Daniel G. Maloney, Marybeth I. Bose, Jeffrey L. Lynd, Lee R. Fenton, Aron W.
Published in
Frontiers in Microbiology
The pyruvate kinase (PYK) isozyme from Thermoanaerobacterium saccharolyticum (TsPYK) has previously been used in metabolic engineering for improved ethanol production. This isozyme belongs to a subclass of PYK isozymes that include an extra C-domain. Like other isozymes that include this extra C-domain, we found that TsPYK is activated by AMP and r...
Kumar, Ammu Prasanna Verma, Chandra S Lukman, Suryani
Published in
Briefings in bioinformatics
Rab proteins represent the largest family of the Rab superfamily guanosine triphosphatase (GTPase). Aberrant human Rab proteins are associated with multiple diseases, including cancers and neurological disorders. Rab subfamily members display subtle conformational variations that render specificity in their physiological functions and can be target...
Pathan-Chhatbar, Salma Drechsler, Carina Richter, Kirsten Morath, Anna Wu, Wei OuYang, Bo Xu, Chenqi Schamel, Wolfgang W
Published in
Frontiers in cell and developmental biology
Biological membranes consist of hundreds of different lipids that together with the embedded transmembrane (TM) proteins organize themselves into small nanodomains. In addition to this function of lipids, TM regions of proteins bind to lipids in a very specific manner, but the function of these TM region-lipid interactions is mostly unknown. In thi...
Mantoni, Federico Scribani Rossi, Chiara Paiardini, Alessandro Di Matteo, Adele Cappellacci, Loredana Petrelli, Riccardo Ricciutelli, Massimo Paone, Alessio Cutruzzolà, Francesca Giardina, Giorgio
...
Published in
Life
GGDEF-containing proteins respond to different environmental cues to finely modulate cyclic diguanylate (c-di-GMP) levels in time and space, making the allosteric control a distinctive trait of the corresponding proteins. The diguanylate cyclase mechanism is emblematic of this control: two GGDEF domains, each binding one GTP molecule, must dimerize...
Dubanevics, Igors McLeish, Tom C B
Published in
Journal of the Royal Society, Interface
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (Mpro, also known as 3CLpro) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bi...
Gobeil, Sophie M-C Janowska, Katarzyna McDowell, Shana Mansouri, Katayoun Parks, Robert Manne, Kartik Stalls, Victoria Kopp, Megan F Henderson, Rory Edwards, Robert J
...
Published in
Cell reports
The severe acute respiratory coronavirus 2 (SARS-CoV-2) spike (S) protein is the target of vaccine design efforts to end the coronavirus disease 2019 (COVID-19) pandemic. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic and are now the dominant form worldwide. Here, we explore S c...
Halder, Anushka Anto, Arinnia Subramanyan, Varsha Bhattacharyya, Moitrayee Vishveshwara, Smitha Vishveshwara, Saraswathi
Network theory-based approaches provide valuable insights into the variations in global structural connectivity between differing dynamical states of proteins. Our objective is to review network-based analyses to elucidate such variations, especially in the context of subtle conformational changes. We present technical details of the construction a...
Bozovic, Olga Zanobini, Claudio Gulzar, Adnan Jankovic, Brankica Buhrke, David Post, Matthias Wolf, Steffen Stock, Gerhard Hamm, Peter
Published in
Proceedings of the National Academy of Sciences of the United States of America
While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site are not well understood. Here the ligand-induced conformational transition in a widely studied model system of a...
