Electrostatic basis for enzyme catalysis

A Warshel, PK Sharma, M Kato, Y Xiang, H Liu… - Chemical …, 2006 - ACS Publications
Enzymatic reactions play a fundamentally important role in controlling and performing most
life processes. 1-3 Thus, understanding how enzymes work has both fundamental and …

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 …

Exploration of reaction pathways and chemical transformation networks

GN Simm, AC Vaucher, M Reiher - The Journal of Physical …, 2018 - ACS Publications
For the investigation of chemical reaction networks, the identification of all relevant
intermediates and elementary reactions is mandatory. Many algorithmic approaches exist …

Context-driven exploration of complex chemical reaction networks

GN Simm, M Reiher - Journal of chemical theory and computation, 2017 - ACS Publications
The construction of a reaction network containing all relevant intermediates and elementary
reactions is necessary for the accurate description of chemical processes. In the case of a …

Nucleic acid polymerases use a general acid for nucleotidyl transfer

C Castro, ED Smidansky, JJ Arnold… - Nature structural & …, 2009 - nature.com
Nucleic acid polymerases catalyze the formation of DNA or RNA from nucleoside-
triphosphate precursors. Amino acid residues in the active site of polymerases are thought to …

Double-proton transfer in adenine− thymine and guanine− cytosine base pairs. A post-hartree− fock ab initio study

L Gorb, Y Podolyan, P Dziekonski… - Journal of the …, 2004 - ACS Publications
The results of a comprehensive study on the double-proton transfer in Adenine− Thymine
(AT) and Guanine− Cytosine (GC) base pairs at room temperature in gas phase and with the …

Critical role of magnesium ions in DNA polymerase β's closing and active site assembly

L Yang, K Arora, WA Beard, SH Wilson… - Journal of the american …, 2004 - ACS Publications
To dissect the effects of the nucleotide-binding and catalytic metal ions on DNA polymerase
mechanisms for DNA repair and synthesis, aside from the chemical reaction, we investigate …

RNA synthesis and capping by non-segmented negative strand RNA viral polymerases: lessons from a prototypic virus

T Ogino, TJ Green - Frontiers in microbiology, 2019 - frontiersin.org
Non-segmented negative strand (NNS) RNA viruses belonging to the order
Mononegavirales are highly diversified eukaryotic viruses including significant human …

Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA-and DNA-dependent RNA and DNA polymerases

C Castro, E Smidansky… - Proceedings of the …, 2007 - National Acad Sciences
The rate-limiting step for nucleotide incorporation in the pre-steady state for most nucleic
acid polymerases is thought to be a conformational change. As a result, very little …

Structure⧸ Function Correlations of Proteins using MM, QM⧸ MM, and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress

A Shurki, A Warshel - Advances in protein chemistry, 2003 - Elsevier
Publisher Summary This chapter focuses on the progress and the current state of
structure/function correlations of biomolecules. One of the primary goals of modern …