A survey of lambda repressor fragments from two-state to downhill folding

Extension-Dependent Drift Velocity and Diffusion (DrDiff) Directly Reconstructs the Folding Free Energy Landscape of Atomic Force Microscopy Experiments

Two equilibrium force microscopy trajectories [q(t)] of high-precision single-molecule spectroscopy assays were analyzed: the pulling of an HIV RNA hairpin and of a 3-aa sequence of the bacteriorhodopsin membrane protein. Both present hundreds of two-state folding transitions, and their free-energy [F(q)] landscapes were previously obtained by deconvolving time signals with the inverse Boltzmann and p_fold methods. In this letter, the two F profiles were reconstructed directly from the measured time-series by the drift-diffusion (DrDiff) framework that characterized the effective conformational drift-velocity [v(q)] and diffusion [D(q)] coefficients. The two thermodynamic F profiles reconstructed with DrDiff directly from q(t) were in good agreement with those previously obtained from the deconvolved time signals. q(t) trajectories simulated with a two-dimensional framework in which the diffusion coefficient of the pulling setup (q coordinate) differed from the molecule (x coordinate) were also analyzed by DrDiff. The performance in reconstructing F was investigated in different conditions of diffusion anisotropy in the simulated time-series using Brownian dynamics. In addition, recently developed theories were used in order to evaluate the quality of the analysis performed in the experimental time series: the memory effects and the intrinsic biomolecular dynamic properties after connecting the probe to the molecule. With the 2-dimensional diffusive models and the additional analyses, it is proposed that the different physical regimes imposed by the stiffer probes of the two biomolecules will have an impact in the measured extension-dependent D and, thus, in the reconstruction of F by DrDiff. Stiffer AFM probes may reflect the molecular behavior more faithfully and reconstruction of F might be more successful. The reported quantities extracted directly from q(t) highlights the current state of the biomolecule characterization by force spectroscopy experiments: it is still challenging despite the recent advances, yet it is very promising.

Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics

As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ_6-85) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix-helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the nonperturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1-3 pair distance displays a slower characteristic time scale than the 1-2 or 3-2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1-3 contact formation indeed is much slower than when monitored by 1-2 or 3-2 contact formation. Unlike the case of the two-state folder [three-α-helix bundle (α₃D)], whose drying and core formation proceed in concert, λ_6-85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non-two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.

Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins

The widespread interest in neutral, water-soluble polymers such as poly(ethylene glycol) (PEG) and poly(zwitterions) such as poly(sulfobetaine) (pSB) for biomedical applications is due to their widely assumed low protein binding. Here we demonstrate that pSB chains in solution can interact with proteins directly. Moreover, pSB can reduce the thermal stability and increase the protein folding cooperativity relative to proteins in buffer or in PEG solutions. Polymer-dependent changes in the tryptophan fluorescence spectra of three structurally-distinct proteins reveal that soluble, 100 kDa pSB interacts directly with all three proteins and changes both the local polarity near tryptophan residues and the protein conformation. Thermal denaturation studies show that the protein melting temperatures decrease by as much as ∼1.9 °C per weight percent of polymer and that protein folding cooperativity increases by as much as ∼130 J mol^-1 K^-1 per weight percent of polymer. The exact extent of the changes is protein-dependent, as some proteins exhibit increased stability, whereas others experience decreased stability at high soluble pSB concentrations. These results suggest that pSB is not universally protein-repellent and that its efficacy in biotechnological applications will depend on the specific proteins used.

Co-translational folding of α-helical proteins: structural studies of intermediate-length variants of the λ repressor

Nascent polypeptide chains fold cotranslationally, but the atomic‐level details of this process remain unknown. Here, we report crystallographic, de novo modeling, and spectroscopic studies of intermediate‐length variants of the λ repressor N‐terminal domain. Although the ranges of helical regions of the half‐length variant were almost identical to those of the full‐length protein, the relative orientations of these helices in the intermediate‐length variants differed. Our results suggest that cotranslational folding of the λ repressor initially forms a helical structure with a transient conformation, as in the case of a molten globule state. This conformation subsequently matures during the course of protein synthesis.

Database

Structural data are available in the PDB under the accession numbers http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5ZCA and http://www.rcsb.org/pdb/search/structidSearch.do?structureId=3WOA.

The Surface of Protein λ6-85 Can Act as a Template for Recurring Poly(ethylene glycol) Structure

PEGylated proteins play an increasingly important role in pharmaceutical drug delivery. We recently showed that short poly(ethylene glycol) (PEG) chains can affect protein structure, even when they are not making extensive contact with the protein surface. In contrast, PEG is generally thought to form a relatively unstructured coil, and its compactness depends on solvent conditions. Here we test whether a host protein could allow PEG to form recurrent structural motifs while the PEG chain is in contact with the protein surface. We link a PEG oligomer (n = 45) to one of two nearly opposite locations on the small α-helical protein λ_6-85 to investigate this question. We first demonstrate experimentally that in these particular positions, PEG does not significantly affect the thermodynamic stability or folding kinetics of λ_6-85. We then use several all-atom molecular dynamics (MD) simulations 1 μs in duration to show how PEG equilibrates between states extending into the solvent and states packed onto the protein surface. The packing reveals recurring structures, including persistent hydrogen bond and hydrophobic contact patterns that appear multiple times. Some interactions of PEG with surface lysines are best described as an "intermittent slithering" motion of the PEG around the side chain, as seen in short MD movies. Thus, PEG achieves a variety of metastable organized structures on the protein surface, somewhere between a random globule and true folding. We also investigated the PEG-protein interaction in the unfolded state of the protein. We find that PEG has a propensity to stabilize certain helices of λ_6-85, no matter which of the two positions it was attached to. Thus, sufficiently long PEG chains are organized by the protein surface and in turn interact with certain elements of protein structure more than others, even when PEG is attached to very different sites.

Globular Protein Folding In Vitro and In Vivo

In vitro, computational, and theoretical studies of protein folding have converged to paint a rich and complex energy landscape. This landscape is sensitively modulated by environmental conditions and subject to evolutionary pressure on protein function. Of these environments, none is more complex than the cell itself, where proteins function in the cytosol, in membranes, and in different compartments. A wide variety of kinetic and thermodynamics experiments, ranging from single-molecule studies to jump kinetics and from nuclear magnetic resonance to imaging on the microscope, have elucidated how protein energy landscapes facilitate folding and how they are subject to evolutionary constraints and environmental perturbation. Here we review some recent developments in the field and refer the reader to some original work and additional reviews that cover this broad topic in protein science.

Molecular dynamics approach to understand the denaturing effect of a millimolar concentration of dodine on a λ-repressor and counteraction by trehalose

Here, we use a molecular dynamics approach to calculate the spatial distribution function of the ternary water–dodine–trehalose (1.0 M) system.

How cooperative are protein folding and unfolding transitions?

A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

The relationship between folding cooperativity and downhill, or barrier-free, folding of proteins under highly stabilizing conditions remains an unresolved topic, especially for proteins such as λ-repressor that fold on the microsecond timescale. Under aqueous conditions where downhill folding is most likely to occur, we measure the stability of multiple H bonds, using hydrogen exchange (HX) in a λYA variant that is suggested to be an incipient downhill folder having an extrapolated folding rate constant of 2 × 10(5) s(-1) and a stability of 7.4 kcal·mol(-1) at 298 K. At least one H bond on each of the three largest helices (α1, α3, and α4) breaks during a common unfolding event that reflects global denaturation. The use of HX enables us to both examine folding under highly stabilizing, native-like conditions and probe the pretransition state region for stable species without the need to initiate the folding reaction. The equivalence of the stability determined at zero and high denaturant indicates that any residual denatured state structure minimally affects the stability even under native conditions. Using our ψ analysis method along with mutational ϕ analysis, we find that the three aforementioned helices are all present in the folding transition state. Hence, the free energy surface has a sufficiently high barrier separating the denatured and native states that folding appears cooperative even under extremely stable and fast folding conditions.

Sequence, structure, and cooperativity in folding of elementary protein structural motifs

Residue-level unfolding of two helix-turn-helix proteins--one naturally occurring and one de novo designed--is reconstructed from multiple sets of site-specific (13)C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa-Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako-Saitô-Muñoz-Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and (13)C-amide I' bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for "experimental" reaction coordinates--namely, the degree of local folding as sensed by site-specific (13)C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.

Mapping fast protein folding with multiple-site fluorescent probes

Fast protein folding involves complex dynamics in many degrees of freedom, yet microsecond folding experiments provide only low-resolution structural information. We enhance the structural resolution of the five-helix bundle protein λ6-85 by engineering into it three fluorescent tryptophan-tyrosine contact probes. The probes report on distances between three different helix pairs: 1-2, 1-3, and 3-2. Temperature jump relaxation experiments on these three mutants reveal two different kinetic timescales: a slower timescale for 1-3 and a faster one for the two contacts involving helix 2. We hypothesize that these differences arise from a single folding mechanism that forms contacts on different timescales, and not from changes of mechanism due to adding the probes. To test this hypothesis, we analyzed the corresponding three distances in one published single-trajectory all-atom molecular-dynamics simulation of a similar mutant. Autocorrelation analysis of the trajectory reveals the same "slow" and "fast" distance change as does experiment, but on a faster timescale; smoothing the trajectory in time shows that this ordering is robust and persists into the microsecond folding timescale. Structural investigation of the all-atom computational data suggests that helix 2 misfolds to produce a short-lived off-pathway trap, in agreement with the experimental finding that the 1-2 and 3-2 distances involving helix 2 contacts form a kinetic grouping distinct from 1 to 3. Our work demonstrates that comparison between experiment and simulation can be extended to several order parameters, providing a stronger mechanistic test.

Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment

Density is an easily adjusted variable in molecular dynamics (MD) simulations. Thus, pressure-jump (P-jump)-induced protein refolding, if it could be made fast enough, would be ideally suited for comparison with MD. Although pressure denaturation perturbs secondary structure less than temperature denaturation, protein refolding after a fast P-jump is not necessarily faster than that after a temperature jump. Recent P-jump refolding experiments on the helix bundle λ-repressor have shown evidence of a <3 μs burst phase, but also of a ~1.5 ms "slow" phase of refolding, attributed to non-native helical structure frustrating microsecond refolding. Here we show that a λ-repressor mutant is nonetheless capable of refolding in a single explicit solvent MD trajectory in about 19 μs, indicating that the burst phase observed in experiments on the same mutant could produce native protein. The simulation reveals that after about 18.5 μs of conformational sampling, the productive structural rearrangement to the native state does not occur in a single swift step but is spread out over a brief series of helix and loop rearrangements that take about 0.9 μs. Our results support the molecular time scale inferred for λ-repressor from near-downhill folding experiments, where transition-state population can be seen experimentally, and also agrees with the transition-state transit time observed in slower folding proteins by single-molecule spectroscopy.

Fast protein folding kinetics

Fast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well <1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even 'slow' folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.

Engineering folding dynamics from two-state to downhill: application to λ-repressor

One strategy for reaching the downhill folding regime, primarily exploited for the λ_6–85 protein fragment, consists of cumulatively introducing mutations that speed up folding. This is an experimentally demanding process where chemical intuition usually serves as a guide for the choice of amino acid residues to mutate. Such an approach can be aided by computational methods that screen for protein engineering hot spots. Here we present one such method that involves sampling the energy landscape of the pseudo-wild-type protein and investigating the effect of point mutations on this landscape. Using a novel metric for the cooperativity, we identify those residues leading to the least cooperative folding. The folding dynamics of the selected mutants are then directly characterized and the differences in the kinetics are analyzed within a Markov-state model framework. Although the method is general, here we present results for a coarse-grained topology-based simulation model of λ-repressor, whose barrier is reduced from an initial value of ∼4k_BT at the midpoint to ∼1k_BT, thereby reaching the downhill folding regime.

Dodine as a protein denaturant: the best of two worlds?

Traditional denaturants such as urea and guanidinium ion unfold proteins in a cooperative "all-or-none" fashion. However, their high working concentration in combination with their strong absorption in the far ultraviolet region make it impossible to measure high quality circular dichroism or infrared spectra, which are commonly used to detect changes in protein secondary structure. On the other hand, detergents such as dodecyl sulfate destabilize native protein conformation at low millimolar concentrations and are UV transparent, but they denature proteins more gradually than guanidinium or urea. In this work, we studied the denaturation properties of the fungicide dodecylguanidinium acetate (dodine), which combines both denaturants into one. We show that dodine unfolds some small proteins at millimolar concentrations, facilitates temperature denaturation, and is transparent enough at its working concentration, unlike guanidinium, to measure full range circular dichroism spectra. Our results also suggest that dodine allows fine-tuning of the protein's unfolded state, unlike traditional "all-or-none" denaturants.

Misplaced helix slows down ultrafast pressure-jump protein folding

Using a newly developed microsecond pressure-jump apparatus, we monitor the refolding kinetics of the helix-stabilized five-helix bundle protein λ*YA, the Y22W/Q33Y/G46,48A mutant of λ-repressor fragment 6-85, from 3 μs to 5 ms after a 1,200-bar P-drop. In addition to a microsecond phase, we observe a slower 1.4-ms phase during refolding to the native state. Unlike temperature denaturation, pressure denaturation produces a highly reversible helix-coil-rich state. This difference highlights the importance of the denatured initial condition in folding experiments and leads us to assign a compact nonnative helical trap as the reason for slower P-jump-induced refolding. To complement the experiments, we performed over 50 μs of all-atom molecular dynamics P-drop refolding simulations with four different force fields. Two of the force fields yield compact nonnative states with misplaced α-helix content within a few microseconds of the P-drop. Our overall conclusion from experiment and simulation is that the pressure-denatured state of λ*YA contains mainly residual helix and little β-sheet; following a fast P-drop, at least some λ*YA forms misplaced helical structure within microseconds. We hypothesize that nonnative helix at helix-turn interfaces traps the protein in compact nonnative conformations. These traps delay the folding of at least some of the population for 1.4 ms en route to the native state. Based on molecular dynamics, we predict specific mutations at the helix-turn interfaces that should speed up refolding from the pressure-denatured state, if this hypothesis is correct.

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization

Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semiempirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics, and sample near-native states in ab initio folding of proteins of ∼100 residues.

Equilibrium unfolding of the PDZ domain of β2-syntrophin

β2-syntrophin, a dystrophin-associated protein, plays a pivotal role in insulin secretion by pancreatic β-cells. It contains a PDZ domain (β2S-PDZ) that, in complex with protein-tyrosine phosphatase ICA512, anchors the dense insulin granules to actin filaments. The phosphorylation state of β2-syntrophin allosterically regulates the affinity of β2S-PDZ for ICA512, and the disruption of the complex triggers the mobilization of the insulin granule stores. Here, we investigate the thermal unfolding of β2S-PDZ at different pH and urea concentrations. Our results indicate that, unlike other PDZ domains, β2S-PDZ is marginally stable. Thermal denaturation experiments show broad transitions and cold denaturation, and a two-state model fit reveals a significant unfolded fraction under physiological conditions. Furthermore, T(m) and T(max) denaturant-dependent shifts and noncoincidence of melting curves monitored at different wavelengths suggest that two-state and three-state models fail to explain the equilibrium data properly and are in better agreement with a downhill scenario. Its higher stability at pH >9 and the results of molecular dynamics simulations indicate that this behavior of β2S-PDZ might be related to its charge distribution. All together, our results suggest a link between the conformational plasticity of the native ensemble of this PDZ domain and the regulation of insulin secretion.

Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations

The five-helix bundle λ-repressor fragment is a fast-folding protein. A length of 80 amino acid residues puts it on the large end among all known microsecond folders and its size poses a computational challenge for molecular dynamics (MD) studies. We simulated the folding of a novel λ-repressor fast-folding mutant (λ-HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observed reversible folding and unfolding of λ-repressor in a 10-microsecond trajectory. The folding kinetics was also investigated through a set of MD simulations run at different temperatures that together covered more than 125 microseconds. The protein was seen to fold into a native-like topology at intermediate temperature and a slow-folding pathway was identified. The simulations suggest new experimental observables for better monitoring the folding process, and a novel mutation expected to accelerate λ-repressor folding.

Crowding effects on the small, fast-folding protein lambda6-85

The microsecond folder lambda6-85 is a small (9.2 kDa = 9200 amu) five helix bundle protein. We investigated the stability of lambda6-85 in two different low-fluorescence crowding matrices: the large 70 kDa carbohydrate Ficoll 70, and the small 14 kDa thermophilic protein SubL. The same thermal stability of secondary structure was measured by circular dichroism in aqueous buffer, and at a crowding fraction phi = 15 +/- 1% of Ficoll 70. Tryptophan fluorescence detection (probing a tertiary contact) yielded the same thermal stability in Ficoll, but 4 degrees C lower in aqueous buffer. Temperature-jump kinetics revealed that the relaxation rate, corrected for bulk viscosity, was very similar in Ficoll and in aqueous buffer. Thus viscosity, hydrodynamics and crowding seem to compensate one another. However, a new fast phase was observed in Ficoll, attributed to crowding-induced downhill folding. We also measured the stability of lambda6-85 in phi = 14 +/- 1% SubL, which acts as a smaller more rigid crowder. Significantly greater stabilization (7 to 13 degrees C depending on probe) was observed than in the Ficoll matrix. The results highlight the importance of crowding agent choice for studies of small, fast-folding proteins amenable to comparison with molecular dynamics simulations.

Hsp90: structure and function

Hsp90 is a highly abundant and ubiquitous molecular chaperone which plays an essential role in many cellular processes including cell cycle control, cell survival, hormone and other signalling pathways. It is important for the cell's response to stress and is a key player in maintaining cellular homeostasis. In the last ten years, it has become a major therapeutic target for cancer, and there has also been increasing interest in it as a therapeutic target in neurodegenerative disorders, and in the development of anti-virals and anti-protozoan infections. The focus of this review is the structural and mechanistic studies which have been performed in order to understand how this important chaperone acts on a wide variety of different proteins (its client proteins) and cellular processes. As with many of the other classes of molecular chaperone, Hsp90 has a critical ATPase activity, and ATP binding and hydrolysis known to modulate the conformational dynamics of the protein. It also uses a host of cochaperones which not only regulate the ATPase activity and conformational dynamics but which also mediate interactions with Hsp90 client proteins. The system is also regulated by post-translational modifications including phosphorylation and acetylation. This review discusses all these aspects of Hsp90 structure and function.

The fast and the slow: folding and trapping of λ6-85

Molecular dynamics simulations combining many microsecond trajectories have recently predicted that a very fast folding protein like lambda repressor fragment λ(6-85) D14A could have a slow millisecond kinetic phase. We investigated this possibility by detecting temperature-jump relaxation to 5 ms. While λ(6-85) D14A has no significant slow phase, two even more stable mutants do. A slow phase of λ(6-85) D14A does appear in mild denaturant. The experimental data and computational modeling together suggest the following hypothesis: λ(6-85) takes only microseconds to reach its native state from an extensively unfolded state, while the latter takes milliseconds to reach compact β-rich traps. λ(6-85) is not only thermodynamically but also kinetically protected from reaching such "intramolecular amyloids" while folding.

Atomistic folding simulations of the five-helix bundle protein λ(6−85)

Protein folding is a classic grand challenge that is relevant to numerous human diseases, such as protein misfolding diseases like Alzheimer’s disease. Solving the folding problem will ultimately require a combination of theory, simulation, and experiment, with theory and simulation providing an atomically detailed picture of both the thermodynamics and kinetics of folding and experimental tests grounding these models in reality. However, theory and simulation generally fall orders of magnitude short of biologically relevant time scales. Here we report significant progress toward closing this gap: an atomistic model of the folding of an 80-residue fragment of the λ repressor protein with explicit solvent that captures dynamics on a 10 milliseconds time scale. In addition, we provide a number of predictions that warrant further experimental investigation. For example, our model’s native state is a kinetic hub, and biexponential kinetics arises from the presence of many free-energy basins separated by barriers of different heights rather than a single low barrier along one reaction coordinate (the previously proposed incipient downhill folding scenario).

Reducing lambda repressor to the core

Lambda repressor fragment λ(*)(6-85) is one of the fastest folding small protein fragments known to date. We hypothesized that removal of three out of five helices of λ(*)(6-85) would further reduce this protein to its smallest folding core. Molecular dynamics simulations singled out two energetically stable reduced structures consisting of only helices 1 and 4 connected by a short glycine/serine linker, as well as a less stable control. We investigated these three polypeptides and their fragments experimentally by using circular dichroism, fluorescence spectroscopy, and temperature jump relaxation spectroscopy to gain insight into their thermodynamic and kinetic properties. Based on the thermal melts, the order of peptide stability was in correspondence with theoretical predictions. The most stable two-helix bundle, λ(blue1), is a cooperatively folding miniprotein with the same melting temperature and folding rate as the full-length λ(*)(6-85) pseudo wild type and a well-defined computed structure.

The folding of single domain proteins--have we reached a consensus?

Rather than stressing the most recent advances in the field, this review highlights the fundamental topics where disagreement remains and where adequate experimental data are lacking. These topics include properties of the denatured state and the role of residual structure, the nature of the fundamental steps and barriers, the extent of pathway heterogeneity and non-native interactions, recent comparisons between theory and experiment, and finally, dynamical properties of the folding reaction.

Challenges in protein folding simulations: Timescale, representation, and analysis

Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.