Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W **, R Nussinov, B Ma - Chemical reviews, 2016‏ - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Is allostery an intrinsic property of all dynamic proteins?

K Gunasekaran, B Ma… - … : Structure, Function, and …, 2004‏ - Wiley Online Library
Allostery involves coupling of conformational changes between two widely separated
binding sites. The common view holds that allosteric proteins are symmetric oligomers, with …

[HTML][HTML] ESPEN micronutrient guideline

MM Berger, A Shenkin, A Schweinlin, K Amrein… - Clinical Nutrition, 2022‏ - Elsevier
Background Trace elements and vitamins, named together micronutrients (MNs), are
essential for human metabolism. Recent research has shown the importance of MNs in …

A unified model of protein dynamics

H Frauenfelder, G Chen, J Berendzen… - Proceedings of the …, 2009‏ - pnas.org
Protein functions require conformational motions. We show here that the dominant
conformational motions are slaved by the hydration shell and the bulk solvent. The protein …

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

I Bahar, TR Lezon, A Bakan, IH Shrivastava - Chemical reviews, 2010‏ - ACS Publications
A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …

Myoglobin: an essential hemoprotein in striated muscle

GA Ordway, DJ Garry - Journal of Experimental Biology, 2004‏ - journals.biologists.com
Myoglobin is a cytoplasmic hemoprotein, expressed solely in cardiac myocytes and
oxidative skeletal muscle fibers, that reversibly binds O2 by its heme residue, a porphyrin …

XFELs for structure and dynamics in biology

JCH Spence - IUCrJ, 2017‏ - journals.iucr.org
The development and application of the free-electron X-ray laser (XFEL) to structure and
dynamics in biology since its inception in 2009 are reviewed. The research opportunities …

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

JD Chodera, N Singhal, VS Pande, KA Dill… - The Journal of …, 2007‏ - pubs.aip.org
To meet the challenge of modeling the conformational dynamics of biological
macromolecules over long time scales, much recent effort has been devoted to constructing …

Slaving: solvent fluctuations dominate protein dynamics and functions

PW Fenimore, H Frauenfelder, BH McMahon… - Proceedings of the …, 2002‏ - pnas.org
Protein motions are essential for function. Comparing protein processes with the dielectric
fluctuations of the surrounding solvent shows that they fall into two classes: nonslaved and …

Multiscale nuclear magnetic relaxation dispersion of complex liquids in bulk and confinement

JP Korb - Progress in Nuclear Magnetic Resonance …, 2018‏ - Elsevier
The nuclear magnetic relaxation dispersion (NMRD) technique consists of measurement of
the magnetic-field dependence of the longitudinal nuclear-spin-lattice relaxation rate 1/T 1 …