The role of protein loops and linkers in conformational dynamics and allostery
Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …
take place on a wide range of time scales. These changes can be as small as the rotation of …
Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …
is often limited by the fact that many systems are characterized by several metastable states …
Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy
The last 15 years have seen a paradigm shift in our understanding of protein biochemistry,
with the realization that an unexpectedly high fraction of the human genome codes for …
with the realization that an unexpectedly high fraction of the human genome codes for …
Expanding the paradigm: intrinsically disordered proteins and allosteric regulation
Allosteric regulatory processes are implicated at all levels of biological function. Recent
advances in our understanding of the diverse and functionally significant class of intrinsically …
advances in our understanding of the diverse and functionally significant class of intrinsically …
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
F Sterpone, S Melchionna, P Tuffery… - Chemical Society …, 2014 - pubs.rsc.org
The OPEP coarse-grained protein model has been applied to a wide range of applications
since its first release 15 years ago. The model, which combines energetic and structural …
since its first release 15 years ago. The model, which combines energetic and structural …
Principles of allosteric interactions in cell signaling
R Nussinov, CJ Tsai, J Liu - Journal of the American Chemical …, 2014 - ACS Publications
Linking cell signaling events to the fundamental physicochemical basis of the
conformational behavior of single molecules and ultimately to cellular function is a key …
conformational behavior of single molecules and ultimately to cellular function is a key …
Accuracy of current all-atom force-fields in modeling protein disordered states
Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered
states that are emerging as crucial actors in many biological processes. Here we assess the …
states that are emerging as crucial actors in many biological processes. Here we assess the …
Unraveling structural mechanisms of allosteric drug action
R Nussinov, CJ Tsai - Trends in pharmacological sciences, 2014 - cell.com
Orthosteric drugs block the active site to obstruct function; allosteric drugs modify the
population of the active state, to modulate function. Available data lead us to propose that …
population of the active state, to modulate function. Available data lead us to propose that …
Molecular recognition by the KIX domain and its role in gene regulation
The kinase-inducible domain interacting (KIX) domain is a highly conserved independently
folding three-helix bundle that serves as a docking site for transcription factors, whereupon …
folding three-helix bundle that serves as a docking site for transcription factors, whereupon …