Precision medicine and driver mutations: computational methods, functional assays and conformational principles for interpreting cancer drivers
At the root of the so-called precision medicine or precision oncology, which is our focus
here, is the hypothesis that cancer treatment would be considerably better if therapies were …
here, is the hypothesis that cancer treatment would be considerably better if therapies were …
The Bio3D packages for structural bioinformatics
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and
dynamics. Major functionality includes biomolecular database searching and retrieval …
dynamics. Major functionality includes biomolecular database searching and retrieval …
Detecting allosteric networks using molecular dynamics simulation
S Bowerman, J Wereszczynski - Methods in enzymology, 2016 - Elsevier
Allosteric networks allow enzymes to transmit information and regulate their catalytic
activities over vast distances. In principle, molecular dynamics (MD) simulations can be used …
activities over vast distances. In principle, molecular dynamics (MD) simulations can be used …
The structural basis of oncogenic mutations G12, G13 and Q61 in small GTPase K-Ras4B
Ras mediates cell proliferation, survival and differentiation. Mutations in K-Ras4B are
predominant at residues G12, G13 and Q61. Even though all impair GAP-assisted GTP→ …
predominant at residues G12, G13 and Q61. Even though all impair GAP-assisted GTP→ …
Residue–residue contact changes during functional processes define allosteric communication pathways
Allosteric regulation plays a central role in orchestrating diverse cellular processes. A
prerequisite for allostery is a flexible biomolecule within which two distal sites can …
prerequisite for allostery is a flexible biomolecule within which two distal sites can …
Oncogenic G12D mutation alters local conformations and dynamics of K-Ras
K-Ras is the most frequently mutated oncoprotein in human cancers, and G12D is its most
prevalent mutation. To understand how G12D mutation impacts K-Ras function, we need to …
prevalent mutation. To understand how G12D mutation impacts K-Ras function, we need to …
Dynamic coupling and allosteric networks in the alpha subunit of heterotrimeric G proteins
Heterotrimeric G proteins operate as intracellular signaling hubs that couple the activation of
cell surface receptors (GPCRs) to the regulation of a multitude of essential cellular …
cell surface receptors (GPCRs) to the regulation of a multitude of essential cellular …
Structural basis of human kinesin-8 function and inhibition
J Locke, AP Joseph, A Peña… - Proceedings of the …, 2017 - National Acad Sciences
Kinesin motors play diverse roles in mitosis and are targets for antimitotic drugs. The clinical
significance of these motors emphasizes the importance of understanding the molecular …
significance of these motors emphasizes the importance of understanding the molecular …
Elucidating allosteric communications in proteins with difference contact network analysis
A difference contact network analysis (dCNA) method is developed for delineating allosteric
mechanisms in proteins. The new method addresses limitations of conventional network …
mechanisms in proteins. The new method addresses limitations of conventional network …
Allosteric communication in the gating mechanism for controlled protein degradation by the bacterial ClpP peptidase
Proteolysis is essential for the control of metabolic pathways and the cell cycle. Bacterial
caseinolytic proteases (Clp) use peptidase components, such as ClpP, to degrade defective …
caseinolytic proteases (Clp) use peptidase components, such as ClpP, to degrade defective …