Protein folding cooperativity: basic insights from minimalist models

Basic concepts about two-state, cooperative protein folding and its relation to first-order phase transitions are reviewed. Minimalist models capable of reproducing the required free energy barrier between folded and unfolded macroscopic states are described. A significantly more restrictive "calorimetric" criterion is also discussed, which is based on direct comparison between model and experimental heat capacities with additional assumptions about conformational enthalpy variation in the unfolded state.     

Driving Protein Conformational Cycles in Physiology and Disease: “Frustrated” Amino Acid Interaction Networks Define Dynamic Energy Landscapes

A general framework by which dynamic interactions within a protein will promote the necessary series of structural changes, or “conformational cycle,” required for function is proposed. It is suggested that the free-energy landscape of a protein is biased toward this conformational cycle. Fluctuations into higher energy, although thermally accessible, conformations drive the conformational cycle forward. The amino acid interaction network is defined as those intraprotein interactions that contribute most to the free-energy landscape. Some network connections are consistent in every structural state, while others periodically change their interaction strength according to the conformational cycle. It is reviewed here that structural transitions change these periodic network connections, which then predisposes the protein toward the next set of network changes, and hence the next structural change. These concepts are illustrated by recent work on tryptophan synthase. Disruption of these dynamic connections may lead to aberrant protein function and disease states.     

Transition networks for modeling the kinetics of conformational change in macromolecules

The kinetics and thermodynamics of complex transitions in biomolecules can be modeled in terms of a network of transitions between the relevant conformational substates. Such a transition network, which overcomes the fundamental limitations of reaction-coordinate-based methods, can be constructed either based on the features of the energy landscape, or from molecular dynamics simulations. Energy-landscape-based networks are generated with the aid of automated path-optimization methods, and, using graph-theoretical adaptive methods, can now be constructed for large molecules such as proteins. Dynamics-based networks, also called Markov State Models, can be interpreted and adaptively improved using statistical concepts, such as the mean first passage time, reactive flux and sampling error analysis. This makes transition networks powerful tools for understanding large-scale conformational changes.     

Quantitative predictions of a noncarrier model for glucose transport across the human red cell membrane

There is an increasing amount of experimental data on transport across biological membranes which cannot be readily accommodated by classical mobile carrier models. We propose models for membrane transport based upon current concepts in molecular enzymology, in which the membrane component involved in transport is an oligomeric protein which undergoes substrate-induced conformational changes. A number of paradoxical observations on glucose transport in the human erythrocyte are explained if the protein involved is a tetramer possessing two classes of binding sites with different affinities for glucose. We develop in detail a particular model of this type, the internal transfer model, in which transport occurs by transfer of substrate from one subunit to another of the protein. The fit of the predictions of the internal transfer model with most of the experimental data is very good. Those data which cannot be fitted by the model cannot be accounted for by any presently available model. We extend our model qualitatively to include the sodium-activated cotransport systems for sugars and amino acids.     

Visualization of drug-nucleic acid interactions at atomic resolution. III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions.

Structural information afforded by the X-ray crystallographic studies of ethidium-dinucleoside monophosphate crystalline complexes described in the preceding two papers has led to a detailed model for ethidium-DNA binding. Features of ethidium-DNA binding, in turn, have led to unifying structural concepts in understanding a wide range of drug-DNA interactions. It is possible that these concepts have still broader implications in understanding the nature of protein-DNA interactions.This paper begins by summarizing the stereochemical aspects of ethidium-DNA, actinomycin-DNA and irehdiamine-DNA binding, molecules that use intercalative and kinked-type geometries in binding to DNA. It then describes superhelical DNA structures formed by kinking DNA periodically varying numbers of base-pairs apart. κ-kinked B DNA, a structure formed by kinking DNA every ten base-pairs, is a left-handed superhelical structure that may be utilized in the organization of DNA within the nucleosome in chromatin. β-kinked B DNA is a right-handed superhelical structure formed by kinking DNA every two base-pairs. It is possible that premelting conformational changes occur in DNA which utilize elements of this structure. This would expose base-pairs to solvent denaturation, and could lower the activation energy necessary for strand separation during DNA denaturation. RNA polymerase and other DNA melting proteins could capitalize on this type of premelting conformational change when binding to DNA.The concept that conformational flexibility exists in DNA structure (and that drug intercalation is a phenomenon that reflects this flexibility) can, in addition, explain a wide variety of physicochemical data about DNA. In this paper we discuss the nature of these data in detail.     

FLIPDock: docking flexible ligands into flexible receptors

Conformational changes of biological macromolecules when binding with ligands have long been observed and remain a challenge for automated docking methods. Here we present a novel protein-ligand docking software called FLIPDock (Flexible LIgand-Protein Docking) allowing the automated docking of flexible ligand molecules into active sites of flexible receptor molecules. In FLIPDock, conformational spaces of molecules are encoded using a data structure that we have developed recently called the Flexibility Tree (FT). While the FT can represent fully flexible ligands, it was initially designed as a hierarchical and multiresolution data structure for the selective encoding of conformational subspaces of large biological macromolecules. These conformational subspaces can be built to span a range of conformations important for the biological activity of a protein. A variety of motions can be combined, ranging from domains moving as rigid bodies or backbone atoms undergoing normal mode-based deformations, to side chains assuming rotameric conformations. In addition, these conformational subspaces are parameterized by a small number of variables which can be searched during the docking process, thus effectively modeling the conformational changes in a flexible receptor. FLIPDock searches the variables using genetic algorithm-based search techniques and evaluates putative docking complexes with a scoring function based on the AutoDock3.05 force-field. In this paper, we describe the concepts behind FLIPDock and the overall architecture of the program. We demonstrate FLIPDock's ability to solve docking problems in which the assumption of a rigid receptor previously prevented the successful docking of known ligands. In particular, we repeat an earlier cross docking experiment and demonstrate an increased success rate of 93.5%, compared to original 72% success rate achieved by AutoDock over the 400 cross-docking calculations. We also demonstrate FLIPDock's ability to handle conformational changes involving backbone motion by docking balanol to an adenosine-binding pocket of protein kinase A.     

MOUSE: A teachable program for learning in conformational analysis

MOUSE is a teachable program which learns concepts of conformational analysis from examples obtained from WIZARD. The algorithms are presented, and a fully worked example is used to demonstrate how MOUSE learns about the so-called “pentane rule.”     

Theoretical studies of protein conformation by means of energy computations

In this review we describe fundamental concepts and applications of conformational energy computations, with emphasis on some recent advances and problems being investigated. The formulation of potential energy functions is described, including the nature of the intramolecular force field, the representation of interactions with the solvent, and considerations of entropy contributions. Approaches to the search for the optimal potential energy are summarized. Examples cited among applications of conformational energy computations include refinement of X-ray crystallographic structures, the use of computations in conjunction with NMR data, prediction of the structures of proteins based on either homology or on other procedures that surmount the multiple-minima problem, the analysis of hierarchical levels of structure and assembly, and interactions in enzyme-substrate complexes.     

Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins

Ligand recombination studies play a central role both for characterizing different hemeproteins and their conformational states but also for probing fundamental biophysical processes. Consequently, there is great importance to providing a foundation from which one can understand the physical processes that give rise to and modulate the large range of kinetic patterns associated with ligand recombination in myoglobins and hemoglobins. In this work, an overview of cryogenic and solution phase recombination phenomena for COMb is first reviewed and then a new paradigm is presented for analyzing the temperature and viscosity dependent features of kinetic traces in terms of multiple phases that reflect which tier(s) of solvent slaved protein dynamics is (are) operative on the photoproduct population during the time course of the measurement. This approach allows for facile inclusion of both ligand diffusion among accessible cavities and conformational relaxation effects. The concepts are illustrated using kinetic traces and MEM populations derived from the CO recombination process for wild type and mutant myoglobins either in sol-gel matrices bathed in glycerol or in trehalose-derived glassy matrices.     

Immobilized stem-loop structured probes as conformational switches for enzymatic detection of microbial 16S rRNA

We have designed and evaluated novel DNA stem-loop structured probes for enzymatic detection of nucleic acid targets. These probes constitute a novel class of conformational switches for enzymatic activity, which in the absence of a target sterically shield an affinity label and upon hybridization of the target to the recognition sequence that forms the loop of the probe restore accessibility of the label for the binding of a reporter enzyme. Analysis of probe characteristics revealed stem stability as the most important parameter governing detection functionality, while other factors such as the length of linker molecules attaching the label to the stem-loop structure and the nature of the solid support proved to be less critical. Apparently, the bulky nature of the reporter enzyme facilitates shielding of the label in the absence of the target, thereby conferring considerable structural tolerance to the conformational switch system. The stem-loop structured probes allow sensitive detection of unlabeled nucleic acid targets. Employing a microtiter assay format, 4 ng of bacterial 16S ribosomal RNA corresponding to 8 fmol could be detected, which can be compared favorably with current immobilized molecular beacon concepts based on fluorescence detection.     

Enzyme fluorescence as a sensing tool: new perspectives in biotechnology

The technology for fluorescence protein-sensing is advancing rapidly owing to the continued introduction of new concepts, new fluorophores, and proteins engineered for sensing-specific analytes. Concerns about the reversibility and selectivity of engineered proteins are being addressed by developing biosensors that are based on the utilisation of coenzyme-depleted enzymes. Such biomolecules do not consume the substrate and can exhibit conformational changes upon the binding of the analyte, which can be easily detected as fluorescence change. In addition, concerns about the stability of biosensors can be overcome by using thermostable enzymes isolated from thermophilic microorganisms. Finally, the development of new techniques such as polarization-based sensing, anisotropy-based sensing and lifetime-based sensing, all of which can be accomplished with light-emitting diodes as the light source, is prompting the design of a new class of specific and stable biosensors, as has occurred with blood glucose measurement. These biosensors represent a valid alternative to the conventional clinical chemistry diagnostics.     

Homology modeling in a dynamical world

A key concept in template‐based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well‐established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved using a priori information coming from the structure‐function relationship. We show that protein families with low conformational diversity show a well‐correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair TBM results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.     

Stress, strain, and mechanotransduction in cells.

It is widely accepted that numerous cell types respond to mechanical stimuli, yet there is no general agreement as to whether particular cells respond directly to stress, strain, strain-rate, strain-energy, or other mechanical quantities. By recalling the definitions of the mathematical (not physical) concepts of stress and strain, it is suggested herein that cells cannot respond directly to these continuum metrics or to quantities derived from them--mechanistic models will need to be based on more fundamental quantities, as, for example, inter-atomic forces or conformational changes of the appropriate molecules. Nonetheless, the concepts of stress and strain should continue to play an important role in mechanobiology, both in the identification of empirical correlations and in the development of phenomenological constitutive models, each of which can contribute to our basic understanding as well as help in the design of future experiments and some clinical interventions. It is important to remember, therefore, that empirical correlations and most constitutive relations in continuum mechanics do not seek to model the actual physics--rather, their utility is in their predictive capability, which is often achieved via different relations in terms of different metrics for the same material under different conditions. Hence, with regard to quantifying cellular responses to mechanical stimuli, we must delineate between the identification of fundamental mechanisms and the formulation of phenomenological correlations, the latter of which only requires convenient metrics that need not be unique or physical.     

VISTRAJ: exploring protein conformational space

VISTRAJ is an application which allows 3D visualization, manipulation and editing of protein conformational space using probabilistic maps of this space called 'trajectory distributions'. Trajectory distributions serve as input to FOLDTRAJ which samples protein structures based on the represented conformational space. VISTRAJ also allows FOLDTRAJ to be used as a tool for homology model creation, and structures may be generated containing post-translationally modified amino acids. AVAILABILITY: Binaries are freely available for non-profit use as part of the FOLDTRAJ package at ftp://ftp.mshri.on.ca/pub/TraDES/foldtraj/.     

Toward nonpeptidal substance P mimetic analogues: design, synthesis, and biological activity.

1,4-Piperazine and 4-hydroxyproline, two small cyclic polyfunctional systems with defined stereochemistry, were introduced as "molecular scaffolds." We define a "bioactive topology," which is a derived putative low-energy conformation obtained through theoretical conformational analysis of substance P. Substitution of these molecular scaffolds by pharmacophors characteristic of the bioactive topology of the C-terminal hexapeptide of substance P resulted in active, partially nonpeptidal substance P mimetic agonists. The study discusses the concepts and tools used to achieve this structural transformation, and points out the need to address flexibility-rigidity issues in an attempt to maintain sufficient molecular plasticity.     

A dye-binding induced conformational transition of poly-(methacrylic acid) by Auramine O in aqueous solutions. II. Theoretical interpretation and discussion of the experimental results

The binding of Auramine O to poly-(methacrylic acid) (PMA) is explained using a two-state model for the polyelectrolyte and preferential binding of the dye to the hypercoiled conformational state of PMA predominantly present for the dye-free polyelectrolyte at low degrees of neutralization. Bound-dye interactions were neglected leading to a binding isotherm as given by Monod et al. to which the experimental dialysis results could be fitted. It is shown that this model predicts a conformational transition from the more extended conformational state of PMA to the hyper-coiled one upon progressive binding of the dye. The experimental results obtained by potentiometric and viscosimetric titrations as well as the fluorcsence intensity measurements of the AuO—PMA system arc consistent with the conclusions based on this model.     

Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer

Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes. Here we discuss the concepts behind the CEST experiment, focusing on practical aspects as well, we review some of the pulse sequences that have been developed to characterize protein and RNA conformational dynamics, and we discuss a number of examples where the CEST methodology has provided important insights into the role of dynamics in biomolecular function.     

Protein adsorption onto nanoparticles induces conformational changes: Particle size dependency,kinetics, and mechanisms

The use of nanomaterials in bioapplications demands a detailed understanding of protein–nanoparticle interactions. Proteins can undergo conformational changes while adsorbing onto nanoparticles, but studies on the impact of particle size on conformational changes are scarce. We have shown that conformational changes happening upon adsorption of myoglobin and BSA are dependent on the size of the nanoparticle they are adsorbing to. Out of eight initially investigated model proteins, two (BSA and myoglobin) showed conformational changes, and in both cases this conformational change was dependent on the size of the nanoparticle. Nanoparticle sizes ranged from 30 to 1000 nm and, in contrast to previous studies, we attempted to use a continuous progression of sizes in the range found in live viruses, which is an interesting size of nanoparticles for the potential use as drug delivery vehicles. Conformational changes were only visible for particles of 200 nm and bigger. Using an optimized circular dichroism protocol allowed us to follow this conformational change with regard to the nanoparticle size and, thanks to the excellent temporal resolution also in time. We uncovered significant differences between the unfolding kinetics of myoglobin and BSA. In this study, we also evaluated the plausibility of commonly used explanations for the phenomenon of nanoparticle size‐dependent conformational change. Currently proposed mechanisms are mostly based on studies done with relatively small particles, and fall short in explaining the behavior seen in our studies.     

The structural basis of secondary active transport mechanisms

Secondary active transporters couple the free energy of the electrochemical potential of one solute to the transmembrane movement of another. As a basic mechanistic explanation for their transport function the model of alternating access was put forward more than 40 years ago, and has been supported by numerous kinetic, biochemical and biophysical studies. According to this model, the transporter exposes its substrate binding site(s) to one side of the membrane or the other during transport catalysis, requiring a substantial conformational change of the carrier protein. In the light of recent structural data for a number of secondary transport proteins, we analyze the model of alternating access in more detail, and correlate it with specific structural and chemical properties of the transporters, such as their assignment to different functional states in the catalytic cycle of the respective transporter, the definition of substrate binding sites, the type of movement of the central part of the carrier harboring the substrate binding site, as well as the impact of symmetry on fold-specific conformational changes. Besides mediating the transmembrane movement of solutes, the mechanism of secondary carriers inherently involves a mechanistic coupling of substrate flux to the electrochemical potential of co-substrate ions or solutes. Mainly because of limitations in resolution of available transporter structures, this important aspect of secondary transport cannot yet be substantiated by structural data to the same extent as the conformational change aspect. We summarize the concepts of coupling in secondary transport and discuss them in the context of the available evidence for ion binding to specific sites and the impact of the ions on the conformational state of the carrier protein, which together lead to mechanistic models for coupling.     

Towards the physical basis of how intrinsic disorder mediates protein function

Intrinsically disordered proteins (IDPs) are an important class of functional proteins that is highly prevalent in biology and has broad association with human diseases. In contrast to structured proteins, free IDPs exist as heterogeneous and dynamical conformational ensembles under physiological conditions. Many concepts have been discussed on how such intrinsic disorder may provide crucial functional advantages, particularly in cellular signaling and regulation. Establishing the physical basis of these proposed phenomena requires not only detailed characterization of the disordered conformational ensembles, but also mechanistic understanding of the roles of various ensemble properties in IDP interaction and regulation. Here, we review the experimental and computational approaches that may be integrated to address many important challenges of establishing a "structural" basis of IDP function, and discuss some of the key emerging ideas on how the conformational ensembles of IDPs may mediate function, especially in coupled binding and folding interactions.