Insights from molecular dynamics simulations for computational protein design

MC Childers, V Daggett - Molecular systems design & engineering, 2017 - pubs.rsc.org
A grand challenge in the field of structural biology is to design and engineer proteins that
exhibit targeted functions. Although much success on this front has been achieved, design …

Protein contact networks: an emerging paradigm in chemistry

L Di Paola, M De Ruvo, P Paci, D Santoni… - Chemical …, 2013 - ACS Publications
Topology is at the very heart of chemistry. This stems from the fact that chemical thought,
since its prescientific alchemic origins, focused on the mutual relations between different …

A lesson for the maestro of the replication fork: targeting the protein‐binding interface of proliferating cell nuclear antigen for anticancer therapy

VK Bhardwaj, R Purohit - Journal of Cellular Biochemistry, 2022 - Wiley Online Library
The proliferating cell nuclear antigen (PCNA) has emerged as a promising candidate for the
development of novel cancer therapeutics. PCNA is a nononcogenic mediator of DNA …

Engineering proteins for thermostability through rigidifying flexible sites

H Yu, H Huang - Biotechnology advances, 2014 - Elsevier
Engineering proteins for thermostability is an exciting and challenging field since it is critical
for broadening the industrial use of recombinant proteins. Thermostability of proteins arises …

Himalayan bioactive molecules as potential entry inhibitors for the human immunodeficiency virus

VK Bhardwaj, R Purohit, S Kumar - Food Chemistry, 2021 - Elsevier
The human immunodeficiency virus interacts with the cluster of differentiation 4 receptors
and one of the two chemokine receptors (CCR5 and CXCR4) to gain entry in human cells …

Directional conformer exchange in dihydrofolate reductase revealed by single-molecule nanopore recordings

NS Galenkamp, A Biesemans, G Maglia - Nature Chemistry, 2020 - nature.com
Conformational heterogeneity is emerging as a defining characteristic of enzyme function.
However, understanding the role of protein conformations requires their thermodynamic and …

Contingency and entrenchment in protein evolution under purifying selection

P Shah, DM McCandlish… - Proceedings of the …, 2015 - National Acad Sciences
The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a
phenomenon known as epistasis. Epistasis can profoundly influence the process of …

Science and art of protein formulation development

W Wang, S Ohtake - International journal of pharmaceutics, 2019 - Elsevier
Protein pharmaceuticals have become a significant class of marketed drug products and are
expected to grow steadily over the next decade. Development of a commercial protein …

Targeting the protein-protein interface pocket of Aurora-A-TPX2 complex: rational drug design and validation

VK Bhardwaj, R Purohit - Journal of Biomolecular Structure and …, 2021 - Taylor & Francis
Aurora-A is a novel therapeutic target that belongs to the serine/threonine kinase family of
proteins. Several cancers are associated with gene amplification or over-expression of …

Advanced protein formulations

W Wang - Protein Science, 2015 - Wiley Online Library
It is well recognized that protein product development is far more challenging than that for
small‐molecule drugs. The major challenges include inherent sensitivity to different types of …