Malladi, Sukhaswami Powell, Harold R. David, Alessia Islam, Suhail A. Copeland, Matthew M. Kundrotas, Petras J. Sternberg, Michael J.E. Vakser, Ilya A.
Published in
Journal of Molecular Biology
Rapid progress in structural modeling of proteins and their interactions is powered by advances in knowledge-based methodologies along with better understanding of physical principles of protein structure and function. The pool of structural data for modeling of proteins and protein–protein complexes is constantly increasing due to the rapid growth...
Nagpal, Sunil Pinna, Nishal Kumar Pant, Namrata Singh, Rohan Srivastava, Divyanshu Mande, Sharmila S.
Published in
Journal of Molecular Biology
Motivation Continuous emergence of new variants through appearance/accumulation/disappearance of mutations is a hallmark of many viral diseases. SARS-CoV-2 variants have particularly exerted tremendous pressure on global healthcare system owing to their life threatening and debilitating implications. The sheer plurality of variants and huge scale o...
Sorokina, Marija Belapure, Jaydeep Tüting, Christian Paschke, Reinhard Papasotiriou, Ioannis Rodrigues, João P.G.L.M. Kastritis, Panagiotis L.
Published in
Journal of Molecular Biology
After two years since the outbreak, the COVID-19 pandemic remains a global public health emergency. SARS-CoV-2 variants with substitutions on the spike (S) protein emerge increasing the risk of immune evasion and cross-species transmission. Here, we analyzed the evolution of the S protein as recorded in 276,712 samples collected before the start of...
Deák, Gauri Cook, Atlanta G.
Published in
Journal of Molecular Biology
Missense variants are alterations to protein coding sequences that result in amino acid substitutions. They can be deleterious if the amino acid is required for maintaining structure or/and function, but are likely to be tolerated at other sites. Consequently, missense variation within a healthy population can mirror the effects of negative selecti...
Patrick, Casey Upadhyay, Vaibhav Lucas, Alexandra Mallela, Krishna M.G.
Published in
Journal of Molecular Biology
Among the five known SARS-CoV-2 variants of concern, Delta is the most virulent leading to severe symptoms and increased mortality among infected people. Our study seeks to examine how the biophysical parameters of the Delta variant correlate to the clinical observations. Receptor binding domain (RBD) is the first point of contact with the human ho...
Lutter, Liisa Al-Hilaly, Youssra K. Serpell, Christopher J. Tuite, Mick F. Wischik, Claude M. Serpell, Louise C. Xue, Wei-Feng
Published in
Journal of Molecular Biology
The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, ...
Cohen, Nir Kahana, Amit Schuldiner, Maya
Published in
Journal of molecular biology
Despite decades of research and the availability of the full genomic sequence of the baker's yeast Saccharomyces cerevisiae, still a large fraction of its genome is not functionally annotated. This hinders our ability to fully understand cellular activity and suggests that many additional processes await discovery. The recent years have shown an ex...
Riziotis, Ioannis G. Ribeiro, António J.M. Borkakoti, Neera Thornton, Janet M.
Published in
Journal of Molecular Biology
Conformational variation in catalytic residues can be captured as alternative snapshots in enzyme crystal structures. Addressing the question of whether active site flexibility is an intrinsic and essential property of enzymes for catalysis, we present a comprehensive study on the 3D variation of active sites of 925 enzyme families, using explicit ...
Mishra, Nawneet Teyra, Joan Boytz, RuthMabel Miersch, Shane Merritt, Trudy N. Cardarelli, Lia Gorelik, Maryna Mihalic, Filip Jemth, Per Davey, Robert A.
...
Published in
Journal of Molecular Biology
The COVID-19 pandemic caused by SARS-CoV-2 infection has impacted the world economy and healthcare infrastructure. Key reagents with high specificity to SARS-CoV-2 proteins are currently lacking, which limits our ability to understand the pathophysiology of SARS-CoV-2 infections. To address this need, we initiated a series of studies to generate an...
Rajah, Maaran Michael Bernier, Annie Buchrieser, Julian Schwartz, Olivier
Published in
Journal of molecular biology
Syncytia are formed when individual cells fuse. SARS-CoV-2 induces syncytia when the viral spike (S) protein on the surface of an infected cell interacts with receptors on neighboring cells. Syncytia may potentially contribute to pathology by facilitating viral dissemination, cytopathicity, immune evasion, and inflammatory response. SARS-CoV-2 vari...
