Model System For Protein Folding Research Articles

The impact of interchain hydrogen bonding on β-hairpin stability is readily predicted by molecular dynamics simulation.

ABSTRACTPeptides are frequently used model systems for protein folding. They are also gaining increased importance as therapeutics. Here, the ability of molecular dynamics (MD) simulation for describing the structure and dynamics of β‐hairpin peptides was investigated, with special attention given to the impact of a single interstrand sidechain to sidechain interaction. The MD trajectories were compared to structural information gained from solution NMR. By assigning frames from restraint‐free MD simulations to an intuitive hydrogen bond on/off pattern, folding ratios and folding pathways were predicted. The computed molecular model successfully reproduces the folding ratios determined by NMR, indicating that MD simulation may be straightforwardly used as a screening tool in β‐hairpin design. © The Authors. Biopolymers Published by Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 703–706, 2015.

Probe the Heme Iron Ligand and Conformational Change of Misfolded States of Cytochrome C through EPR Spectroscopy

Cytochrome c is a heme-protein existing in the membrane of mitochrondria which plays a pivotal role in apoptosis. Besides its important biological functions, it is a model system for protein folding and unfolding studies. Recently, Soffer et al. [Soffer et al. Biochemistry 2013, 52, 1397−1408] claimed that a meta-stable misfolded state of horse heart ferricytochreome c could be obtained after exposing the protein to the ferricyanide solution at very alkaline pH for an extended period of time, and it did not undergo any remarkable change in its secondary and tertiary structures upon adjusting the solution to folding promoting conditions at neutral pH. Yet the axial coordination of the heme iron as well as the electronic structures for the misfolded protein remained undetermined. For this purpose, in this work, electron paramagnetic resonance (EPR) spectra of the misfolded protein in the solution at different pH values were recorded, and DFT calculation was conducted to predict the EPR g-tensor at different axial ligand configurations. Our EPR data indicate that the misfolded protein at very alkaline condition exhibits a hexacoordinated low spin state, while at pH 5 the protein adapt the configuration similar to the native-like low-spin ferric heme complex which possesses a histidine/methionine coordination environment. For pH value between 6 and 7, the EPR spectra appear to be the superposition of the two species. With the aid of DFT calculation, also checked by the EPR and other spectroscopic data, the possible hexacoordinated low spin state with a hydroxyl ion as the proximal ligand and the pentacoordinated quantum mixed state of the heme iron for misfolded protein at different folding conditions were discussed. This work was partially supported by Hundred Talents Program of Chinese Academy of Sciences.

Observing and Characterizing Early Folding Intermediates of E.Coli Rnase H using Kinetic and Equilibrium Approaches

E. coli ribonuclease H has been an important model system for protein folding for many years. It has long been known that it folds through an intermediate (Icore) en route to the native state. However, because folding to Icore occurs on the fast millisecond timescale, and there is very little Icore populated under equilibrium conditions, key questions have remained unanswered: What is the nature of the folding pathway en route to Icore, and how well packed is Icore?In this work, a new ultrarapid mixing technique coupled with time-correlated single photon counting detection of intrinsic fluorescence allows observation of the millisecond folding to Icore, including new early intermediates formed along the way. Mutagenesis and hydrogen exchange methods provide structural information about these new early intermediates. Additionally, two equilibrium models of Icore are made and characterized, providing new insight into the nature of this intermediate. This work increases our knowledge about the folding pathway and energy landscape of an important protein folding model system, at a time- and size-scale that is amenable to comparison with protein folding simulations.

NMR assignments of PI3-SH3 domain aided by protonless NMR spectroscopy

We report here the near complete assignments of native bovine PI3-SH3 domain, which has been a model system for protein folding, misfolding and amyloid fibril formation. The use of (13)C-detected protonless NMR spectroscopy is instrumental in assigning the spin system of the proline residue at the C-terminus in addition to the missing resonances in proton-based NMR spectra due to rapid solvent exchange. It also helps assign the resonances of all three proline amine nitrogen nuclei, which are underrepresented in the database. Comparison of the backbone (13)C resonances of PI3-SH3 in its native and amyloid fibril states shows that the aggregation of PI3-SH3 is accompanied by major conformational rearrangements.

Dynamics and Mechanism of Membrane-Induced Folding of a Small Beta-Hairpin

A complementary approach of experiments and computation were used to characterize the dynamics and mechanism of peptide folding and insertion into the membrane. SVS-1, an 18-residue anti-cancer peptide that is designed to be disordered in solution, but fold into a β-hairpin at an anionic bilayer surface, was used as a model system for protein folding on the membrane. Infrared and fluorescence where used to characterize the folding of the peptide in the membrane. Laser induced temperature-jumps (T-jump) were used to initiate the folding reaction. Computational models of tryptophan-containing SVS-1 mutants were used to guide the choice of targets for fluorescent studies. Molecular dynamic simulations model the folded and unfolded states at the bilayer surface to estimate timescales of binding, folding and insertion. Simulations were used to interpret and guide future experiments.

Challenges in protein-folding simulations

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.

How to Arm a Supervillin: Designing F-Actin Binding Activity into Supervillin Headpiece

Villin-type headpiece domains are compact motifs that have been used extensively as model systems for protein folding. Although the majority of headpiece domains bind actin, there are some that lack this activity. Here, we present the first NMR solution structure and 15N-relaxation analysis of a villin-type headpiece domain natively devoid of F-actin binding activity, that of supervillin headpiece (SVHP). The structure was found to be similar to that of other headpiece domains that bind F-actin. Our NMR analysis demonstrates that SVHP lacks a conformationally flexible region (V-loop) present in all other villin-type headpiece domains and which is essential to the phosphoryl regulation of dematin headpiece. In comparing the electrostatic surface potential map of SVHP to that of other villin-type headpiece domains with significant affinity for F-actin, we identified a positive surface potential conserved among headpiece domains that bind F-actin but absent from SVHP. A single point mutation (L38K) in SVHP, which creates a similar positive surface potential, endowed SVHP with specific affinity for F-actin that is within an order of magnitude of the tightest binding headpiece domains. We propose that this effect is likely conferred by a specific buried salt bridge between headpiece and actin. As no high-resolution structural information exists for the villin-type headpiece F-actin complex, our results demonstrate that through positive mutagenesis, it is possible to design binding activity into homologous proteins without structural information of the counterpart's binding surface.

Experimental monitoring and data analysis tools for protein folding: Study of steady-state evolution and modeling of kinetic transients by multitechnique and multiexperiment data fusion

Protein folding is a complex process that can take place through different pathways depending on the inducing agent and on the monitored time scale. This diversity of possibilities requires a good design of experiments and powerful data analysis tools that allow operating with multitechnique measurements and/or with diverse experiments related to different aspects of the process of interest. Multivariate curve resolution–alternating least squares (MCR–ALS) has been the core methodology used to perform multitechnique and/or multiexperiment data analysis. This algorithm allows for obtaining the process concentration profiles and pure spectra of all species involved in the protein folding from the sole raw spectroscopic measurements obtained during the experimental monitoring. The process profiles provide insight on the mechanism of the process studied whereas the shapes of the recovered pure spectra help in the characterization of the protein conformations involved. Relevant features of the MCR–ALS algorithm are the possibility to handle fused data, i.e., series of experiments monitored with different techniques and/or performed under different experimental conditions, and the flexibility to include a priori information linked to general properties of concentration profiles and spectra and to the kinetic model governing the folding process. All these characteristics help to obtain a comprehensive description of the protein folding mechanism. To our knowledge, this work includes for the first time the simultaneous analysis of steady-state and short-time scale kinetic experiments linked to a protein folding process. The potential of this methodology is shown taking myoglobin as a model system for protein folding or, in general, for the study of any complex biological process that needs multitechnique and multiexperiment monitoring and analysis. Transformations in myoglobin due to changes in pH have been monitored by ultraviolet/visible (UV–vis) absorption and circular dichroism (CD) spectroscopy. Steady-state and stopped-flow experiments were carried out to account for the evolution of the process at different time scales. In this example, the multiexperiment analysis has allowed for the reliable detection and modeling of a kinetic transient species in the myoglobin folding process, absent in the steady-state working conditions.

Correlation between Protein Stability Cores and Protein Folding Kinetics: A Case Study on Pseudomonas aeruginosa Apo-Azurin

This paper reports a combined computational and experimental study of the correlation between protein stability cores and folding kinetics. An empirical potential function was developed, and it was used for analyzing interaction energies among secondary structure elements. Studies on a beta sandwich protein, Pseudomonas aeruginosa azurin, showed that the computationally identified substructure with the strongest interactions in the native state is identical to the "interlocked pair" of beta strands, an invariant motif found in most sandwich-like proteins. Moreover, previous and new in vitro folding results revealed that the identified substructure harbors most residues that form native-like interactions in the folding transition state. These observations demonstrate that the potential function is effective in revealing the relative strength of interactions among various protein parts; they also strengthen the suggestion that the most stable regions in native proteins favor stable interactions early during folding.

Hidden complexity of free energy surfaces for peptide (protein) folding.

An understanding of the thermodynamics and kinetics of protein folding requires a knowledge of the free energy surface governing the motion of the polypeptide chain. Because of the many degrees of freedom involved, surfaces projected on only one or two progress variables are generally used in descriptions of the folding reaction. Such projections result in relatively smooth surfaces, but they could mask the complexity of the unprojected surface. Here we introduce an approach to determine the actual (unprojected) free energy surface and apply it to the second beta-hairpin of protein G, which has been used as a model system for protein folding. The surface is represented by a disconnectivity graph calculated from a long equilibrium folding-unfolding trajectory. The denatured state is found to have multiple low free energy basins. Nevertheless, the peptide shows exponential kinetics in folding to the native basin. Projected surfaces obtained from the present analysis have a simple form in agreement with other studies of the beta-hairpin. The hidden complexity found for the beta-hairpin surface suggests that the standard funnel picture of protein folding should be revisited.

Cytochrome c551 as a model system for protein folding

Considerable progress was made over the last few years in understanding the mechanism of folding of cytochrome c551, a small acidic hemeprotein from Pseudomonas aeruginosa. Comparison of our results with those obtained by others on horse heart cytochrome c allows to draw some general conclusions on the structural features that are common determinants in the folding of members of the cytochrome c family.

Native-state energetics of a thermostabilized variant of ribonuclease HI

Escherichia coli RNase HI is a well-characterized model system for protein folding and stability. Controlling protein stability is critical for both natural proteins and for the development of engineered proteins that function under extreme conditions. We have used native-state hydrogen exchange on a variant containing the stabilizing mutation Asp10 to alanine in order to determine its residue-specific stabilities. On average, the ΔGunf value for each residue was increased by 2-3 kcal/mol, resulting in a lower relative population of partially unfolded forms. Though increased in stability by a uniform factor, D10A shows a distribution of stabilities in its secondary structural units that is similar to that of E. coli RNase H, but not the closely related protein from Thermus thermophilus. Hence, the simple mutation used to stabilize the enzyme does not recreate the balance of conformational flexibility evolved in the thermophilic protein.

Stability and folding of dihydrofolate reductase from the hyperthermophilic bacterium Thermotoga maritima.

Dihydrofolate reductase (DHFR) has been a well-established model system for protein folding. The enzyme DHFR from the hyperthermophilic bacterium Thermotoga maritima (TmDHFR) displays distinct adaptations toward high temperatures at the level of both structure and stability. The enzyme represents an extremely stable dimer; no isolated structured monomers could be detected in equilibrium or during unfolding. The equilibrium unfolding strictly follows the two-state model for a dimer (N(2) right harpoon over left harpoon 2U), with a free energy of stabilization of DeltaG = -142 +/- 10 kJ/mol at 15 degrees C. The two-state model is applicable over the whole temperature range (5-70 degrees C), yielding a DeltaG vs T profile with maximum stability at around 35 degrees C. There is no flattening of the stability profile. Instead, the enhanced thermostability is characterized by shifts toward higher overall stability and higher temperature of maximum stability. TmDHFR unfolds in a highly cooperative manner via a nativelike transition state without intermediates. The unfolding reaction is much slower (ca. 10(8) times) compared to DHFR from Escherichia coli (EcDHFR). In contrast to EcDHFR, no evidence for heterogeneity of the native state is detectable. Refolding proceeds via at least two intermediates and a burst-phase of rather low amplitude. Reassociation of monomeric intermediates is not rate-limiting on the folding pathway due to the high association constant of the dimer.

Dissection of the de novo designed peptide alpha t alpha: stability and properties of the intact molecule and its constituent helices.

Alpha t alpha is a de novo designed 38-residue peptide [Fezoui et al. (1995) Protein Sci. 4, 286-295] that adopts a helical hairpin conformation in solution [Fezoui et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 3675-3679; Fezoui et al. (1997) Protein Sci. 6, 1869-1877]. Since alpha t alpha was developed as a model system for protein folding at the stage where secondary structures interact and become mutually stabilizing, it is of interest to investigate the increase in stability that occurs with helix association. alpha t alpha was dissected into its component helices and the relative stabilities of the individual helices and the parent molecule were assessed. The Delta G0 of unfolding of alpha t alpha measured by guanidine hydrochloride denaturation was determined to be 3.4 kcal/mol. The equilibrium constant for folding of alpha t alpha was estimated from the Delta G0 as 338 and from hydrogen exchange measurements as 259. The stability of the helices in intact alpha t alpha over the individual helices increased by a factor of at least 37 based on amide proton exchange measurements. Sedimentation equilibrium studies showed very little association of the peptides to form either homo- or heterodimers, suggesting that helix association is stabilized by the high effective concentration of the helices caused by the presence of the connecting turn. The effects of salt and pH on the helicity of the component peptides are largely reflected in the intact molecule, implying that short-range interactions still make important contributions to the conformation of the intact molecule even though significant stabilization is caused by helix association.

Strategies and rationales for the de novo design of a helical hairpin peptide

The de novo design of alpha t alpha, a helical hairpin peptide, is described, alpha t alpha (alpha-helix/turn/alpha-helix) was developed to provide a model system for protein folding at the level of secondary structure association and stabilization. According to the prevailing models of protein folding, the second step in the folding process is the association and stabilization of secondary structural elements or microdomains. A brief description of the design, along with CD and NMR evidence confirming the conformation of the peptide in solution, has been published (Fezoui Y, Weaver DL, Osterhout JJ, 1994, Proc Natl Acad Sci USA 91:3675-3679). The present work includes a full description of the design process, including the trade-offs that were made during the development of the peptide, a discussion of recent experimental results that were not available at the time of the original design, indications of areas where, in retrospect, the design might have been done differently, and a discussion of how the present work fits into the field of de novo protein design.

Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helixes of myoglobin

Myoglobin has been extensively studied as a model system for protein folding in vitro. As part of an ongoing study of myoglobin folding, we have synthesized a series of peptide fragments corresponding to portions of the sequence of the sperm whale protein. The conformational preferences of these peptides have been investigated by circular dichroism and nuclear magnetic resonance spectroscopy in aqueous solution. In this paper we describe the folding propensities of two peptides (Mb-G and Mb-H), corresponding to the G- and H-helix segments of the myoglobin sequence. The Mb-G peptide shows evidence of a very small population of helical conformations in aqueous solution, both by CD and NMR. By contrast, the monomeric Mb-H peptide is found by CD to adopt a significant population (ca. 30%) of ordered helix and by NMR to populate helical conformations in rapid dynamic equilibrium with unfolded states. The Mb-H peptide undergoes a well-characterized, concentration-dependent monomer-tetramer equilibrium. At peptide concentrations greater than 1 mM there is an increase in the population of helix, to approximately 85% according to the CD spectrum, through self-association to form a tetramer. Both medium-range NOE connectivities and a CD spectrum characteristic of ordered helix are observed at low peptide concentrations, establishing that helical conformations are present in the monomeric state of Mb-H. The relative helicity at various sites throughout the Mb-H peptide has been estimated using a novel method for assessing the distribution of helical populations based on the relative magnitudes of medium-range d alpha beta (i,i+3) NOE connectivities. The population of ordered helix is seen to be highest in the center of the peptide sequence; the ends of the peptide show evidence of pronounced fraying.