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 …

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 …

Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics

L Iversen, HL Tu, WC Lin, SM Christensen, SM Abel… - Science, 2014 - science.org
Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of
Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation …

Calculations of the electric fields in liquid solutions

SD Fried, LP Wang, SG Boxer, P Ren… - The Journal of Physical …, 2013 - ACS Publications
The electric field created by a condensed-phase environment is a powerful and convenient
descriptor for intermolecular interactions. Not only does it provide a unifying language to …

Sizing up single-molecule enzymatic conformational dynamics

HP Lu - Chemical Society Reviews, 2014 - pubs.rsc.org
Enzymatic reactions and related protein conformational dynamics are complex and
inhomogeneous, playing crucial roles in biological functions. The relationship between …

On the relationship between folding and chemical landscapes in enzyme catalysis

M Roca, B Messer, D Hilvert… - Proceedings of the …, 2008 - National Acad Sciences
Elucidating the relationship between the folding landscape of enzymes and their catalytic
power has been one of the challenges of modern enzymology. The present work explores …

Rethinking vibrational stark spectroscopy: Peak shifts, line widths, and the role of non-stark solvent coupling

SM Fica-Contreras, AP Charnay, J Pan… - The Journal of …, 2023 - ACS Publications
A vibration's transition frequency is partly determined by the first-order Stark effect, which
accounts for the electric field experienced by the mode. Using ultrafast infrared pump–probe …

Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy

Q Guo, Y He, HP Lu - … of the National Academy of Sciences, 2015 - National Acad Sciences
Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical
in understanding the structure–function relationship and enzymatic reaction dynamics …

Probing single-molecule enzyme active-site conformational state intermittent coherence

Y He, Y Li, S Mukherjee, Y Wu, H Yan… - Journal of the American …, 2011 - ACS Publications
The relationship between protein conformational dynamics and enzymatic reactions has
been a fundamental focus in modern enzymology. Using single-molecule fluorescence …

Dielectric fluctuations in force microscopy: Noncontact friction and frequency jitter

SM Yazdanian, JA Marohn, RF Loring - The Journal of chemical …, 2008 - pubs.aip.org
Electric force microscopy, in which a charged probe oscillates tens to hundreds of
nanometers above a sample surface, provides direct mechanical detection of relaxation in …