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 …

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 …

[HTML][HTML] Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

A Warshel, RP Bora - The Journal of chemical physics, 2016 - pubs.aip.org
Enzymes control chemical reactions that are key to life processes, and allow them to take
place on the time scale needed for synchronization between the relevant reaction cycles. In …

Structure and mechanism of DNA polymerase β

WA Beard, SH Wilson - Chemical reviews, 2006 - ACS Publications
Cells throughout nature contain multiple and overlapping DNA repair pathways that are
essential for maintaining the integrity of genomic DNA. 1, 2 The DNA repair pathway known …

[HTML][HTML] 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 …

A new paradigm for DNA polymerase specificity

YC Tsai, KA Johnson - Biochemistry, 2006 - ACS Publications
We show that T7 DNA polymerase exists in three distinct structural states, as reported by a
conformationally sensitive fluorophore attached to the recognition (fingers) domain. The …

[HTML][HTML] 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 …

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 …

How DNA polymerases catalyse replication and repair with contrasting fidelity

WJ Wu, W Yang, MD Tsai - Nature Reviews Chemistry, 2017 - nature.com
DNA polymerases were named for their function of catalysing DNA replication, a process
that is necessary for growth and propagation of life. DNA involving Watson–Crick base …