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 …

QM/MM methods for biological systems

HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …

N-Ras forms dimers at POPC membranes

J Güldenhaupt, T Rudack, P Bachler, D Mann… - Biophysical journal, 2012 - cell.com
Ras is a central regulator of cellular signaling pathways. It is mutated in 20–30% of human
tumors. To perform its function, Ras has to be bound to a membrane by a posttranslationally …

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

M Klähn, S Braun-Sand, E Rosta… - The Journal of Physical …, 2005 - ACS Publications
Reliable studies of enzymatic reactions by combined quantum mechanics/molecular
mechanics (QM/MM) approaches, with an ab initio description of the quantum region …

Structural basis of effector regulation and signal termination in heterotrimeric Gα proteins

SR Sprang, Z Chen, X Du - Advances in protein chemistry, 2007 - Elsevier
This chapter addresses, from a molecular structural perspective gained from examination of
x‐ray crystallographic and biochemical data, the mechanisms by which GTP‐bound Gα …

Target-related applications of first principles quantum chemical methods in drug design

A Cavalli, P Carloni, M Recanatini - Chemical reviews, 2006 - ACS Publications
A fundamental postulate in the classical drug design paradigm is that the effect of a drug in
the human body is a consequence of the molecular recognition between a ligand (the drug) …

[HTML][HTML] Modeling the mechanisms of biological GTP hydrolysis

ATP Carvalho, K Szeler, K Vavitsas, J Åqvist… - Archives of Biochemistry …, 2015 - Elsevier
Enzymes that hydrolyze GTP are currently in the spotlight, due to their molecular switch
mechanism that controls many cellular processes. One of the best-known classes of these …

Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations

T Rudack, F **a, J Schlitter, C Kötting… - Proceedings of the …, 2012 - pnas.org
Members of the Ras superfamily regulate many cellular processes. They are down-
regulated by a GTPase reaction in which GTP is cleaved into GDP and P i by nucleophilic …

Metal fluorides as analogues for studies on phosphoryl transfer enzymes

Y **, NG Richards, JP Waltho… - Angewandte Chemie …, 2017 - Wiley Online Library
The 1994 structure of a transition‐state analogue with AlF4− and GDP complexed to G1α, a
small G protein, heralded a new field of research into the structure and mechanism of …

Hydrolysis of guanosine triphosphate (GTP) by the Ras· GAP protein complex: reaction mechanism and kinetic scheme

MG Khrenova, BL Grigorenko… - The Journal of …, 2015 - ACS Publications
Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine
diphosphate (GDP) and inorganic phosphate (Pi) by the Ras· GAP protein complex are fully …