Nonspecific binding—fundamental concepts and consequences for biosensing applications

A Frutiger, A Tanno, S Hwu, RF Tiefenauer… - Chemical …, 2021 - ACS Publications
Nature achieves differentiation of specific and nonspecific binding in molecular interactions
through precise control of biomolecules in space and time. Artificial systems such as …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Native contacts determine protein folding mechanisms in atomistic simulations

RB Best, G Hummer, WA Eaton - Proceedings of the …, 2013 - National Acad Sciences
The recent availability of long equilibrium simulations of protein folding in atomistic detail for
more than 10 proteins allows us to identify the key interactions driving folding. We find that …

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

P Csermely, R Palotai, R Nussinov - Trends in biochemical sciences, 2010 - cell.com
Single molecule and NMR measurements of protein dynamics increasingly uncover the
complexity of binding scenarios. Here, we describe an extended conformational selection …

Water mediation in protein folding and molecular recognition

Y Levy, JN Onuchic - Annu. Rev. Biophys. Biomol. Struct., 2006 - annualreviews.org
Water is essential for life in many ways, and without it biomolecules might no longer truly be
biomolecules. In particular, water is important to the structure, stability, dynamics, and …

Mechanism of coupled folding and binding of an intrinsically disordered protein

K Sugase, HJ Dyson, PE Wright - Nature, 2007 - nature.com
Protein folding and binding are analogous processes, in which the protein 'searches' for
favourable intramolecular or intermolecular interactions on a funnelled energy landscape …

Fundamental aspects of protein− protein association kinetics

G Schreiber, G Haran, HX Zhou - Chemical reviews, 2009 - ACS Publications
The structure of a protein complex together with information about its affinity and other
thermodynamic characteristics provide a “frozen” view of the complex. This picture ignores …

Transient protein–protein interactions

SE Acuner Ozbabacan, HB Engin… - … , Design & Selection, 2011 - academic.oup.com
Transient complexes are crucial for diverse biological processes such as biochemical
pathways and signaling cascades in the cell. Here, we give an overview of the transient …

[HTML][HTML] Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization

Y Shan, MP Eastwood, X Zhang, ET Kim, A Arkhipov… - Cell, 2012 - cell.com
The mutation and overexpression of the epidermal growth factor receptor (EGFR) are
associated with the development of a variety of cancers, making this prototypical …

An all‐atom structure‐based potential for proteins: bridging minimal models with all‐atom empirical forcefields

PC Whitford, JK Noel, S Gosavi, A Schug… - Proteins: Structure …, 2009 - Wiley Online Library
Protein dynamics take place on many time and length scales. Coarse‐grained structure‐
based \bf(G\overlineo) models utilize the funneled energy landscape theory of protein …