Special issue on protein folding: Experimental and theoretical approaches

Abstract

Proteins are complex objects able to organize themselves in many different conformations with well-defined motions that are directly involved in biological function. Therefore, protein folding must be composed, in detail, of a complicated network of reactions. Still, it has been described by experimentalists in terms of simple empirical patterns such as linear free energy relationships. This apparent simplicity is a consequence of the global organization of the landscape of energies of protein conformations into a funnel. The field of protein folding has gone through a scientific revolution for about two decades. Our modern understanding of this problem based on energy landscape theory and the funnel concept describes folding as the progressive evolution of an ensemble of partially folded structures through which the protein moves on its way to the native structure. The development of this new understanding of protein folding would be impossible simply by theory and simulation. A new generation of experiments has probed and verified the protein funnel landscape, the existence of minimal frustration and, as a consequence, that the transition state ensemble (viz. the variation in the amount of local native structure) is primarily determined by topological constraints. They have also shown that although a funneled landscape is responsible for the protein folding ability, many different detailed mechanisms must be and have been observed. In the spirit of this new theoretical framework based on energy landscape theory and the funnel concept, a perspective by Wolynes and collaborators discusses the large ensemble of conformational substates of proteins. They comment that since most experiments probe only the low free energy states, this provides a spectrum of excitations that appear simpler than reality. In a funnel-like energy landscape, partially unfolded states compose most of the important excitations but frustration and symmetry are additional alternatives for low free energy excitations. Also guided by energy landscape theory, the perspective by Munoz and collaborators discusses the experimental evidences for one of the great predictions of this theory, the possibility of downhill folding. The article by Levy and collaborators comments on the nature of the unfolded ensemble that in a funnel-like landscape is stabilized by residual native interactions. In the case of repeat proteins, they suggest that this stabilization may also come from non-native contacts, a situation that appears to be less likely for small globular proteins. The protein folding funnel is not perfectly smooth and therefore has some residual ruggedness. The article by Lapidus and collaborators quantifies this ruggedness for the case of protein L. In the early states of energy landscape theory, most of the studies were focused on small fast folding proteins. Lattice models have played a major role in these early developments. As an example see the article by Mann and collaborators. Recently, one has moved towards more exciting and larger systems. The perspective by Clarke and collaborators focuses on the folding of multidomain proteins and investigates how folding can be controlled by individual domains and interactions among them. The article by Jackson and collaborators deals with the folding of green fluorescence protein. This protein has a very complex landscape, where the initial fast folding is followed by very slow events in a superstable core. The perspective by Oliverberg and collaborator connects folding and disease. It discusses how folding and aggregation of the enzyme superoxide dismutase may be responsible for the disease amyotropic lateral sclerosis (ALS). They show that ALS-provoking mutations decrease either protein stability or net repulsive charge—the classical hallmarks for a disease mechanism triggered by association of non-native proteins. The perspective by Aguzzi and collaborators continues on the topic of folding∕misfolding and disease and reviews current techniques for studying prion strain differences in vivo and in cells, and the knowledge gained from modeling prion fibril growth in vitro and in simple organisms. Finally, all these advances in our understanding of protein folding would be impossible without the development of completely new experimental advances that have allowed for probing in details the energy landscape. In this issue some of the most recent and amazing new techniques are described. The perspective by Gruebele and collaborators comments on the novel technique of terahertz spectroscopy, which allows for directly probing protein induced changes in the collective water network. They comment how the solvation shell appears to influence more the native protein than the unfolded or mutated one. The commentary by Ormos discusses how the new technique of two-dimensional-infrared permits the observation of dynamical phenomena directly. This technique has the potential of directly relating structure and detailed dynamics experimentally. The commentary by Schneider discusses how new high-flux x-ray techniques have created the ability of determining protein structure in small crystals; something that was impossible in the near past. Also showing new progress in structural biology, the perspective by Engelman describes recent progress in electron microscopy with particular emphasis on challenges in fitting high-resolution structures into electron microscopic reconstructions. This issue includes an amazing collection of contributions describing the most recent advances in protein folding. The evolution of this field during the last 20 years has been enormous and has shown how theoreticians and experimentalists working together can really transform a field of research. I strongly enjoyed working as a Guest Editor for this special issue. I enjoyed reading every commentary, perspective, and article of this issue and I am certain that you, the reader, will also enjoy reading the articles in this issue. I deeply thank everybody that made this issue possible, especially the authors for their great contributions!