Why nature really chose phosphate

SCL Kamerlin, PK Sharma, RB Prasad… - Quarterly reviews of …, 2013‏ - cambridge.org
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and
maintaining the integrity of the genetic material. On the surface, it would appear to be a …

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

SCL Kamerlin, A Warshel - Proteins: Structure, Function, and …, 2010‏ - Wiley Online Library
Enzymes play a key role in almost all biological processes, accelerating a variety of
metabolic reactions as well as controlling energy transduction, the transcription, and …

Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials

Z Benayad, R David, G Stirnemann - … of the National Academy of Sciences, 2024‏ - pnas.org
While RNA appears as a good candidate for the first autocatalytic systems preceding the
emergence of modern life, the synthesis of RNA oligonucleotides without enzymes remains …

Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions

N Singh, A Warshel - Proteins: Structure, Function, and …, 2010‏ - Wiley Online Library
Calculating the absolute binding free energies is a challenging task. Reliable estimates of
binding free energies should provide a guide for rational drug design. It should also provide …

Conformational dynamics modulate the catalytic activity of the molecular chaperone Hsp90

SL Mader, A Lopez, J Lawatscheck, Q Luo… - Nature …, 2020‏ - nature.com
The heat shock protein 90 (Hsp90) is a molecular chaperone that employs the free energy of
ATP hydrolysis to control the folding and activation of several client proteins in the eukaryotic …

ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism

CL Parke, EJ Wojcik, DK Worthylake, S Kim - Biophysical Journal, 2010‏ - cell.com
Motor proteins couple steps in ATP binding and hydrolysis to conformational switching both
in and remote from the active site. In our kinesin• AMPPNP crystal structure, closure of the …

Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis

F Duarte, J Åqvist, NH Williams… - Journal of the American …, 2015‏ - ACS Publications
Understanding phosphoryl and sulfuryl transfer is central to many biochemical processes.
However, despite decades of experimental and computational studies, a consensus …

ATP analogues for structural investigations: case studies of a DnaB helicase and an ABC transporter

D Lacabanne, T Wiegand, N Wili, MI Kozlova… - Molecules, 2020‏ - mdpi.com
Nucleoside triphosphates (NTPs) are used as chemical energy source in a variety of cell
systems. Structural snapshots along the NTP hydrolysis reaction coordinate are typically …

Mechanistic roles of metal-and ligand-protonated species in hydrogen evolution with [Cp* Rh] complexes

WC Henke, Y Peng, AA Meier, E Fujita… - Proceedings of the …, 2023‏ - pnas.org
Protonation reactions involving organometallic complexes are ubiquitous in redox chemistry
and often result in the generation of reactive metal hydrides. However, some organometallic …

Nucleophilic substitution at phosphorus: stereochemistry and mechanisms

OI Kolodiazhnyi, A Kolodiazhna - Tetrahedron: Asymmetry, 2017‏ - Elsevier
This review is devoted to the stereochemistry of nucleophilic substitution reactions at
phosphorus. The study of the reactions of phosphoryl group transfer is important for …