The role of dynamic conformational ensembles in biomolecular recognition

DD Boehr, R Nussinov, PE Wright - Nature chemical biology, 2009 - nature.com
Molecular recognition is central to all biological processes. For the past 50 years,
Koshland's' induced fit'hypothesis has been the textbook explanation for molecular …

[HTML][HTML] NMR tools to detect protein allostery

O Gampp, H Kadavath, R Riek - Current Opinion in Structural Biology, 2024 - Elsevier
Allostery is a fundamental mechanism of cellular homeostasis by intra-protein
communication between distinct functional sites. It is an internal process of proteins to steer …

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

OF Lange, NA Lakomek, C Fares, GF Schroder… - science, 2008 - science.org
Protein dynamics are essential for protein function, and yet it has been challenging to
access the underlying atomic motions in solution on nanosecond-to-microsecond time …

Structural biology by NMR: structure, dynamics, and interactions

PRL Markwick, T Malliavin, M Nilges - PLoS computational …, 2008 - journals.plos.org
The function of bio-macromolecules is determined by both their 3D structure and
conformational dynamics. These molecules are inherently flexible systems displaying a …

Combining experimental and simulation data of molecular processes via augmented Markov models

S Olsson, H Wu, F Paul… - Proceedings of the …, 2017 - National Acad Sciences
Accurate mechanistic description of structural changes in biomolecules is an increasingly
important topic in structural and chemical biology. Markov models have emerged as a …

The use of residual dipolar coupling in studying proteins by NMR

K Chen, N Tjandra - NMR of Proteins and Small Biomolecules, 2012 - Springer
The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a
decade ago, has become a useful and almost routine tool for accurate protein solution …

Two-dimensional infrared spectroscopy of photoswitchable peptides

P Hamm, J Helbing, J Bredenbeck - Annu. Rev. Phys. Chem., 2008 - annualreviews.org
We present a detailed discussion of the complimentary fields of the application of two-
dimensional infrared (2D-IR) spectroscopy in comparison with two-dimensional nuclear …

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

RB Fenwick, S Esteban-Martín, X Salvatella - European Biophysics Journal, 2011 - Springer
We review the role conformational ensembles can play in the analysis of biomolecular
dynamics, molecular recognition, and allostery. We introduce currently available methods for …

A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy

XC Su, B Man, S Beeren, H Liang… - Journal of the …, 2008 - ACS Publications
A new lanthanide tag was designed for site-specific labeling of proteins with paramagnetic
lanthanide ions. The tag, 4-mercaptomethyl-dipicolinic acid, binds lanthanide ions with …

Conformational flexibility of a microcrystalline globular protein: order parameters by solid-state NMR spectroscopy

JL Lorieau, AE McDermott - Journal of the American Chemical …, 2006 - ACS Publications
The majority of protein structures are determined in the crystalline state, yet few methods
exist for the characterization of dynamics for crystalline biomolecules. Solid-state NMR can …