Theory of protein folding: the energy landscape perspective

JN Onuchic, Z Luthey-Schulten… - Annual review of …, 1997 - annualreviews.org
▪ Abstract The energy landscape theory of protein folding is a statistical description of a
protein's potential surface. It assumes that folding occurs through organizing an ensemble of …

Principles of protein folding—a perspective from simple exact models

KA Dill, S Bromberg, K Yue, HS Chan… - Protein …, 1995 - Wiley Online Library
General principles of protein structure, stability, and folding kinetics have recently been
explored in computer simulations of simple exact lattice models. These models represent …

Funnels, pathways, and the energy landscape of protein folding: a synthesis

JD Bryngelson, JN Onuchic, ND Socci… - Proteins: Structure …, 1995 - Wiley Online Library
The understanding, and even the description of protein folding is impeded by the complexity
of the process. Much of this complexity can be described and understood by taking a …

Theory of protein folding

JN Onuchic, PG Wolynes - Current opinion in structural biology, 2004 - Elsevier
Protein folding should be complex. Proteins organize themselves into specific three-
dimensional structures, through a myriad of conformational changes. The classical view of …

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism

BA Shoemaker, JJ Portman… - Proceedings of the …, 2000 - National Acad Sciences
Protein folding and binding are kindred processes. Many proteins in the cell are unfolded, so
folding and function are coupled. This paper investigates how binding kinetics is influenced …

How does a protein fold?

AS˘ ali, E Shakhnovich, M Karplus - nature, 1994 - nature.com
THE number of all possible conformations of a polypeptide chain is too large to be sampled
exhaustively. Nevertheless, protein sequences do fold into unique native states in seconds …

The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics

OM Becker, M Karplus - The Journal of chemical physics, 1997 - pubs.aip.org
Topological characteristics of multidimensional potential energy surfaces are explored and
the full conformation space is mapped on the set of local minima. This map partitions …

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 …

Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics

HT Nguyen, N Hori, D Thirumalai - Nature chemistry, 2022 - nature.com
Although it is known that RNA undergoes liquid–liquid phase separation, the interplay
between the molecular driving forces and the emergent features of the condensates, such as …

Molecular crowding enhances native state stability and refolding rates of globular proteins

MS Cheung, D Klimov… - Proceedings of the …, 2005 - National Acad Sciences
The presence of macromolecules in cells geometrically restricts the available space for
poplypeptide chains. To study the effects of macromolecular crowding on folding …