Is the molten globule a third phase of proteins?

Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins

Transitions between the unfolded and native states of the ordered globular proteins are accompanied by the accumulation of several intermediates, such as pre-molten globules, wet molten globules, and dry molten globules. Structurally equivalent conformations can serve as native functional states of intrinsically disordered proteins. This overview captures the characteristics and importance of these molten globules in both structured and intrinsically disordered proteins. It also discusses examples of engineered molten globules. The formation of these intermediates under conditions of macromolecular crowding and their interactions with nanomaterials are also reviewed.

A surprisingly simple three-state generic process for reversible protein denaturation by trifluoroethanol

Despite the rich knowledge of the influence of 2,2,2-trifluoroethanol (TFE) on the structure and conformation of peptides and proteins, the mode(s) of TFE-protein interactions and the mechanism by which TFE reversibly denatures a globular protein remain elusive. This study systematically examines TFE-induced equilibrium transition curves for six paradigmatic globular proteins by using basic fluorescence and circular dichroism measurements under neutral pH conditions. The results are remarkably simple. Low TFE invariably unfolds the tertiary structure of all proteins to produce the obligate intermediate (I) which retains nearly all of native-state secondary structure, but enables the formation of extra α-helices as the level of TFE is raised higher. Inspection of the transitions at once reveals that the tertiary structure unfolding is always a distinct process, necessitating the inclusion of at least one obligate intermediate in the TFE-induced protein denaturation. It appears that the intermediate in the minimal unfolding mechanism N⇌I⇌D somehow acquires higher α-helical propensity to generate α-helices in excess of that in the native state to produce the denatured state (D), also called the TFE state. The low TFE-populated intermediate I may be called a universal intermediate by virtue of its α-helical propensity. Contrary to many earlier suggestions, this study dismisses molten globule (MG)-like attribute of I or D.

The Molten Globule State of a Globular Protein in a Cell Is More or Less Frequent Case Rather than an Exception

Quite a long time ago, Oleg B. Ptitsyn put forward a hypothesis about the possible functional significance of the molten globule (MG) state for the functioning of proteins. MG is an intermediate between the unfolded and the native state of a protein. Its experimental detection and investigation in a cell are extremely difficult. In the last decades, intensive studies have demonstrated that the MG-like state of some globular proteins arises from either their modifications or interactions with protein partners or other cell components. This review summarizes such reports. In many cases, MG was evidenced to be functionally important. Thus, the MG state is quite common for functional cellular proteins. This supports Ptitsyn’s hypothesis that some globular proteins may switch between two active states, rigid (N) and soft (MG), to work in solution or interact with partners.

High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants

The spliceosome protein U1A is a prototype case of the RNA recognition motif (RRM) ubiquitous in biological systems. The in vitro kinetics of the chemical denaturation of U1A indicate that the unfolding of U1A is a two-state process but takes place via high energy channeling and a malleable transition state, an interesting variation of typical two-state behavior. Molecular dynamics (MD) simulations have been applied extensively to the study of two-state unfolding and folding of proteins and provide an opportunity to obtain a theoretical account of the experimental results and a molecular model for the transition state ensemble. We describe herein all-atom MD studies including explicit solvent of up to 100 ns on the thermal unfolding (UF) of U1A and 13 mutants. Multiple MD UF trajectories are carried out to ensure accuracy and reproducibility. A vector representation of the MD unfolding process in RMSD space is obtained and used to calculate a free energy landscape for U1A unfolding. A corresponding MD simulation and free energy landscape for the protein CI2, well known to follow a simple two state folding/unfolding model, is provided as a control. The results indicate that the unfolding pathway on the MD calculated free energy landscape of U1A shows a markedly extended transition state compared with that of CI2. The MD results support the interpretation of the observed chevron plots for U1A in terms of a high energy, channel-like transition state. Analysis of the MDUF structures shows that the transition state ensemble involves microstates with most of the RRM secondary structure intact but expanded by ~14% with respect to the radius of gyration. Comparison with results on a prototype system indicates that the transition state involves an ensemble of molten globule structures and extends over the region of ~1-35 ns in the trajectories. Additional MDUF simulations were carried out for 13 U1A mutants, and the calculated φ-values show close accord with observed results and serve to validate our methodology.

Complex Inclusion Bodies and Defective Proteome Hubs in Neurodegenerative Disease: New Clues, New Challenges

A healthy physiological environment of cells represents the dynamic homeostasis of crowded molecules. A subset of cellular proteome forms protein quality control (PQC) machinery to maintain an uninterrupted synthesis of new polypeptides and targeted elimination of old or defective proteins. The process of PQC may get overwhelmed under specific genetic mutations, environmental stress conditions, and aging-associated perturbances. Many of these conditions may lead to the generation of various types of aberrant protein species that may or may not accumulate as large cellular inclusions. These proteinaceous formations, referred to as inclusion bodies (IBs), could be membrane-bound or membrane-less, cytoplasmic, or nuclear. Most importantly, they could either be toxic or protective. Under acute stress conditions, the formation of aggregates may cause proteostasis failure, leading to large-scale changes in the cellular proteome compositions. However, the large insoluble IBs may act as reservoirs for many soluble proteins with high aggregation propensities, which can overwhelm the cellular chaperoning capacity and protein degradation machinery. The kinetic equilibrium between folding and unfolding, misfolding, and refolding; aggregation and degradation is perturbed in one or many neurodegenerative disorders (NDDs) associated with dementia, cognitive impairments, movement, and behavioural losses. However, a detailed interplay of IBs into the manifestation of the NDDs is unknown, and a very primitive knowledge of structural compositions of amyloid inclusions is present. The present article presents a brief evolutionary background of IBs; their functional relevance for prokaryotes, plants, and animals; and associated involvement in neuronal proteostasis.

Singlet oxygen quenching as a probe for cytochrome c molten globule state formation

Singlet oxygen refers to the nonradical metastable excited state of molecular oxygen that readily oxidizes various cellular components. Its behavior in different biological systems has been studied for many years. Recently, we analyzed the effect of singlet oxygen quenching by heme cofactor in cytochrome c (cyt c). Here, we have exploited this effect in the investigation of conformational differences in the molten globule states of cyt c induced by different sodium anions, namely sulfate, chloride and perchlorate. The high efficiency of heme toward quenching singlet oxygen enabled us to use this property for the analysis of the otherwise experimentally difficult-to-determine parameter of heme upon exposure to solvents as highly similar conformational states of cyt c in the molten globule states are induced by different salts at acidic pH. Our results from singlet oxygen quenching experiments correlate well with other spectroscopic methods, such as circular dichroism and fluorescence measurements, and suggest increasing availability of heme in the order: perchlorate < chloride < sulfate. Based on our findings we propose that singlet oxygen phosphorescence measurements are useful in determining the differences in the protein conformation of their heme regions, particularly regarding the relative heme exposure to the solvent.

Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective Variable

Recently, we have shown that the residue folding degree, a network-based measure of folded content in proteins, is able to capture backbone conformational transitions related to the formation of secondary structures in molecular dynamics (MD) simulations. In this work, we focus primarily on developing a collective variable (CV) for MD based on this residue-bound parameter to be able to trace the evolution of secondary structure in segments of the protein. We show that this CV can do just that and that the related energy profiles (potentials of mean force, PMF) and transition barriers are comparable to those found by others for particular events in the folding process of the model mini protein Trp-cage. Hence, we conclude that the relative segment folding degree (the newly proposed CV) is a computationally viable option to gain insight into the formation of secondary structures in protein dynamics. We also show that this CV can be directly used as a measure of the amount of α-helical content in a selected segment.

Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction

Fast kinetic experiments with dramatically improved time resolution have contributed significantly to understanding the fundamental processes in protein folding pathways involving the formation of a-helices and b-hairpin, contact formation, and overall collapse of the peptide chain. Interpretation of experimental results through application of a simple statistical mechanical model was key to this understanding. Atomistic description of all events observed in the experimental findings was challenging. Recent advancements in theory, more sophisticated algorithms, and a true long-term trajectory made way for an atomically detailed description of kinetics, examining folding pathways, validating experimental results, and reporting new findings for a wide range of molecular processes in biophysical chemistry. This review describes how optimum dimensionality reduction theory can construct a simplified coarse-grained model with low dimensionality involving a kinetic matrix that captures novel insights into folding pathways. A set of metastable states derived from molecular dynamics analysis generate an optimally reduced dimensionality rate matrix following transition pathway analysis. Analysis of the actual long-term simulation trajectory extracts a relaxation time directly comparable to the experimental results and confirms the validity of the combined approach. The application of the theory is discussed and illustrated using several examples of helix <==> coil transition pathways. This paper focuses primarily on a combined approach of time-resolved experiments and long-term molecular dynamics simulation from our ongoing work.

Process, Outcomes and Possible Elimination of Aggregation with Special Reference to Heme Proteins; Likely Remediations of Proteinopathies

Protein folding is a natural phenomenon through which a linear polypeptide possessing necessary information attains three-dimension functionally active conformation. This is a complex and multistep process and therefore, the presence of several intermediary structures could be speculated as a result of protein folding. In in vivo, this folding process is governed by the assistance of other proteins called molecular chaperones and heat shock proteins. Due to the mechanism of protein folding, these intermediary structures remain major challenge for modern biology. Mutation in gene encoding amino acid can cause adverse environmental conditions which may result in misfolding of the linear polypeptide followed by the formation of aggregates and amyloidosis. Aggregation contributes to the pathophysiology of several maladies including diabetes mellitus, Huntington's and Alzheimer's disease. The propensity of native structure to form aggregated and fibrillar assemblies is a hallmark of amyloidosis. During aggregation of a protein, transition from α helix to β sheet is observed, and mainly β sheeted structure is visualised in a mature fibril. Heme proteins are very crucial for major life activities like transport of oxygen and carbon dioxide, synthesis of ATP, role in electron transport chain, and detoxification of free radicals formed during biochemical reactions. Any structural variation in the heme proteins may lead to a fatal response. Hence characterization of the folding intermediates becomes crucial. The characterization has been deciphered with the help of strong denaturants like acetonitrile and TFE. Moreover, possible role of elimination of these aggregates and prevention of protein denaturation is also discussed. Current review deals with the basic process and mechanism of the protein folding in general and the ultimate outcomes of the protein misfolding. Since Native conformation of heme proteins is essential for some vital activities as listed above, we have discussed possible prevention of denaturation and aggregation of heme proteins such as Hb, cyt c, catalase & peroxidase.

Mechanobiology: protein refolding under force

The application of direct force to a protein enables to probe wide regions of its energy surface through conformational transitions as unfolding, extending, recoiling, collapsing, and refolding. While unfolding under force typically displayed a two-state behavior, refolding under force, from highly extended unfolded states, displayed a more complex behavior. The first recording of protein refolding at a force quench step displayed an initial rapid elastic recoil, followed by a plateau phase at some extension, concluding with a collapse to a final state, at which refolding occurred. These findings stirred a lively discussion, which led to further experimental and theoretical investigation of this behavior. It was demonstrated that the polymeric chain of the unfolded protein is required to fully collapse to a globular conformation for the maturation of native structure. This behavior was modeled using one-dimensional free energy landscape over the end-to-end length reaction coordinate, the collective measured variable. However, at low forces, conformational space is not well captured by such models, and using two-dimensional energy surfaces provides further insight into the dynamics of this process. This work reviews the main concepts of protein refolding under constant force, which is essential for understanding how mechanotransducing proteins operate in vivo.

Physical and thermodynamic characterization of the rice gibberellin receptor/gibberellin/DELLA protein complex

Gibberellins (GAs) are phytohormones that regulate various developmental processes in plants. The initial GA signalling events involve the binding of a GA to the soluble GA receptor protein GID1, followed by the binding of the complex to the negative transcriptional regulator of GA signaling, the DELLA protein. Although X-ray structures for certain Arabidopsis GID1/GA/DELLA protein complexes have previously been determined, examination of these complexes did not fully clarify how a DELLA protein recognizes and binds to a GID1/GA complex. Herein, we present a study aimed at physically defining, via a combination of gel chromatography, isothermal titration calorimetry (ITC), small-angle X-ray scattering experiments (SAXS), NMR spectroscopy and mutagenesis, how the rice DELLA protein (SLR1) binds to the rice GID1/GA complex. We have identified the shortest SLR1 sequence (M28-A112) that binds the rice GID/GA complex tightly. The binding constant for the ternary complex that includes SLR1(M28-A112) is 2.9 × 10⁷ M⁻¹; the binding is enthalpically driven and does not depend on the chemical nature of the bound GA. Furthermore, the results of SAXS, ITC, and gel filtration experiments indicate that when free in solution, SLR1(M28-A112) is a natively unfolded protein. The NMR experiments expand this observation to show that the unfolded mutant also contains a small amount of marginally stable secondary structure. Conversely, the protein has a highly ordered structure when bound one-to-one to GID1/GA.

Exploring the pH-Induced Functional Phase Space of Human Serum Albumin by EPR Spectroscopy

A systematic study on the self-assembled solution system of human serum albumin (HSA) and paramagnetic doxyl stearic acid (5-DSA and 16-DSA) ligands is reported covering the broad pH range 0.7–12.9, mainly using electron paramagnetic resonance (EPR) methods. It is tested to which extent the pH-induced conformational isomers of HSA reveal themselves in continuous wave (CW) EPR spectra from this spin probing approach in comparison to an established spin-labeling strategy utilizing 3-maleimido proxyl (5-MSL). Most analyses are conducted on empirical levels with robust strategies that allow for the detection of dynamic changes of ligand, as well as protein. Special emphasis has been placed on the EPR spectroscopic detection of a molten globule (MG) state of HSA that is typically found by the fluorescent probe 8-Anilino- naphthalene-1-sulfonic acid (ANS). Moreover, four-pulse double electron-electron resonance (DEER) experiments are conducted and substantiated with dynamic light scattering (DLS) data to determine changes in the solution shape of HSA with pH. All results are ultimately combined in a detailed scheme that describes the pH-induced functional phase space of HSA.

Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers

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Virus-membrane fusion proteins have vital role in MERS CoV replication.

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Both trimers and monomers were found in both of virus and cell membranes.

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Changes in MERS CoV heptad repeat domains monomers and trimers were resolved by MD simulation.

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Monomer was unstable, having high RMSDs with major drifts above 8 Å.

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Trimer is more dynamically stable with very low RMSD.

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulations were carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lower root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HRs, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer was modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the a and d positions of HR helices stabilize the whole system, with minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at the a and d positions of HR helix were strong stabilizers of HR recognition.

Simulated Force Quench Dynamics Shows GB1 Protein Is Not a Two State Folder

Single molecule force spectroscopy is a useful technique for investigating mechanically induced protein unfolding and refolding under reduced forces by monitoring the end-to-end distance of the protein. The data is often interpreted via a "two-state" model based on the assumption that the end-to-end distance alone is a good reaction coordinate and the thermodynamic behavior is then ascribed to the free energy as a function of this one reaction coordinate. In this paper, we determined the free energy surface (PMF) of GB1 protein from atomistic simulations in explicit solvent under different applied forces as a function of two collective variables (the end-to-end-distance, and the fraction of native contacts ρ). The calculated 2-d free energy surfaces exhibited several distinct states, or basins, mostly visible along the ρ coordinate. Brownian dynamics (BD) simulations on the smoothed free energy surface show that the protein visits a metastable molten globule state and is thus a three state folder, not the two state folder inferred using the end-to-end distance as the sole reaction coordinate. This study lends support to recent experiments that suggest that GB1 is not a two-state folder.

Effect of non-specific interactions on formation and stability of specific complexes

We introduce a simple model to describe the interplay between specific and non-specific interactions. We study the influence of various physical factors on the static and dynamic properties of the specific interactions of our model and show that contrary to intuitive expectations, non-specific interactions can assist in the formation of specific complexes and increase their stability. We then discuss the relevance of these results for biological systems.

A new concept for molecular engineering of artificial enzymes: a multiscale simulation

We propose a new concept for the design of artificial enzymes from synthetic protein-like copolymers and non-natural functional monomers which in terms of their affinity for water can be divided into two categories: hydrophobic and hydrophilic. Hydrophilic monomers comprise catalytically active groups similar to those in the corresponding amino acid residues. A key ingredient of our approach is that the target globular conformation of protein-like, core-shell morphology with multiple catalytic groups appears spontaneously in the course of controlled radical polymerization in a selective solvent. As a proof of concept, we construct a fully synthetic analog of serine hydrolase, e.g.α-chymotrypsin, using the conformation-dependent sequence design approach and multiscale simulation that combines the methods of "mesoscale chemistry" and atomistic molecular dynamics (MD). A 100 ns GPU-accelerated MD simulation of the designed polymer-supported catalyst in the aqueous environment provides valuable information on the structural organization of this system that has been synthesized in our Lab.

Gradual Folding of an Off-Pathway Molten Globule Detected at the Single-Molecule Level

Molten globules (MGs) are compact, partially folded intermediates that are transiently present during folding of many proteins. These intermediates reside on or off the folding pathway to native protein. Conformational evolution during folding of off-pathway MGs is largely unexplored. Here, we characterize the denaturant-dependent structure of apoflavodoxin's off-pathway MG. Using single-molecule fluorescence resonance energy transfer (smFRET), we follow conversion of unfolded species into MG down to denaturant concentrations that favor formation of native protein. Under strongly denaturing conditions, fluorescence resonance energy transfer histograms show a single peak, arising from unfolded protein. The smFRET efficiency distribution shifts to higher value upon decreasing denaturant concentration because the MG folds. Strikingly, upon approaching native conditions, the fluorescence resonance energy transfer efficiency of the MG rises above that of native protein. Thus, smFRET exposes the misfolded nature of apoflavodoxin's off-pathway MG. We show that conversion of unfolded into MG protein is a gradual, second-order-like process that simultaneously involves separate regions within the polypeptide.

DNA binding properties of the small cascade subunit Csa5

CRISPR-Cas systems provide immunity against viral attacks in archaeal and bacterial cells. Type I systems employ a Cas protein complex termed Cascade, which utilizes small CRISPR RNAs to detect and degrade the exogenic DNA. A small sequence motif, the PAM, marks the foreign substrates. Previously, a recombinant type I-A Cascade complex from the archaeon Thermoproteus tenax was shown to target and degrade DNA in vitro, dependent on a native PAM sequence. Here, we present the biochemical analysis of the small subunit, Csa5, of this Cascade complex. T. tenax Csa5 preferentially bound ssDNA and mutants that showed decreased ssDNA-binding and reduced Cascade-mediated DNA cleavage were identified. Csa5 oligomerization prevented DNA binding. Specific recognition of the PAM sequence was not observed. Phylogenetic analyses identified Csa5 as a universal member of type I-A systems and revealed three distinct groups. A potential role of Csa5 in R-loop stabilization is discussed.

Detecting selection on protein stability through statistical mechanical models of folding and evolution

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change.

Differential role of molten globule and protein folding in distinguishing unique features of botulinum neurotoxin

Botulinum neurotoxins (BoNTs) are proteins of great interest not only because of their extreme toxicity but also paradoxically for their therapeutic applications. All the known serotypes (A-G) have varying degrees of longevity and potency inside the neuronal cell. Differential chemical modifications such as phosphorylation and ubiquitination have been suggested as possible mechanisms for their longevity, but the molecular basis of the longevity remains unclear. Since the endopeptidase domain (light chain; LC) of toxin apparently survives inside the neuronal cells for months, it is important to examine the structural features of this domain to understand its resistance to intracellular degradation. Published crystal structures (both botulinum neurotoxins and endopeptidase domain) have not provided adequate explanation for the intracellular longevity of the domain. Structural features obtained from spectroscopic analysis of LCA and LCB were similar, and a PRIME (PReImminent Molten Globule Enzyme) conformation appears to be responsible for their optimal enzymatic activity at 37°C. LCE, on the other hand, was although optimally active at 37°C, but its active conformation differed from the PRIME conformation of LCA and LCB. This study establishes and confirms our earlier finding that an optimally active conformation of these proteins in the form of PRIME exists for the most poisonous poison, botulinum neurotoxin. There are substantial variations in the structural and functional characteristics of these active molten globule related structures among the three BoNT endopeptidases examined. These differential conformations of LCs are important in understanding the fundamental structural features of proteins, and their possible connection to intracellular longevity could provide significant clues for devising new countermeasures and effective therapeutics.

Kinetic Analysis of Guanidine Hydrochloride Inactivation of β-Galactosidase in the Presence of Galactose

Inactivation of purified β-Galactosidase was done with GdnHCl in the absence and presence of varying [galactose] at 50°C and at pH 4.5. Lineweaver-Burk plots of initial velocity data, in the presence and absence of guanidine hydrochloride (GdnHCl) and galactose, were used to determine the relevant K_m and V_max values, with p-nitrophenyl β-D-galactopyranoside (pNPG) as substrate, S. Plots of ln([P]_∞ − [P]_t) against time in the presence of GdnHCl yielded the inactivation rate constant, A. Plots of A versus [S] at different galactose concentrations were straight lines that became increasingly less steep as the [galactose] increased, showing that A was dependent on [S]. Slopes and intercepts of the 1/[P]_∞ versus 1/[S] yielded k₊₀ and k'₊₀, the microscopic rate constants for the free enzyme and the enzyme-substrate complex, respectively. Plots of k₊₀ and k'₊₀ versus [galactose] showed that galactose protected the free enzyme as well as the enzyme-substrate complex (only at the lowest and highest [galactose]) against GdnHCl inactivation. In the absence of galactose, GdnHCl exhibited some degree of non-competitive inhibition. In the presence of GdnHCl, galactose exhibited competitive inhibition at the lower [galactose] of 5 mM which changed to non-competitive as the [galactose] increased. The implications of our findings are further discussed.

Defective protein folding and aggregation as the basis of neurodegenerative diseases: the darker aspect of proteins

The ability of a polypeptide to fold into a unique, functional, and three-dimensional structure depends on the intrinsic properties of the amino acid sequence, function of the molecular chaperones, proteins, and enzymes. Every polypeptide has a finite tendency to misfold and this forms the darker side of the protein world. Partially folded and misfolded proteins that escape the cellular quality control mechanism have the high tendency to form inter-molecular hydrogen bonding between the same protein molecules resulting in aggregation. This review summarizes the underlying and universal mechanism of protein folding. It also deals with the factors responsible for protein misfolding and aggregation. This article describes some of the consequences of such behavior particularly in the context of neurodegenerative conformational diseases such as Alzheimer's, Parkinson's, Huntington's, amyotrophic lateral sclerosis and other non-neurodegenerative conformational diseases such as cancer and cystic fibrosis etc. This will encourage a more proactive approach to the early diagnosis of conformational diseases and nutritional counseling for patients.

Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape

Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.

Direct visualization reveals dynamics of a transient intermediate during protein assembly

Interactions between proteins underlie numerous biological functions. Theoretical work suggests that protein interactions initiate with formation of transient intermediates that subsequently relax to specific, stable complexes. However, the nature and roles of these transient intermediates have remained elusive. Here, we characterized the global structure, dynamics, and stability of a transient, on-pathway intermediate during complex assembly between the Signal Recognition Particle (SRP) and its receptor. We show that this intermediate has overlapping but distinct interaction interfaces from that of the final complex, and it is stabilized by long-range electrostatic interactions. A wide distribution of conformations is explored by the intermediate; this distribution becomes more restricted in the final complex and is further regulated by the cargo of SRP. These results suggest a funnel-shaped energy landscape for protein interactions, and they provide a framework for understanding the role of transient intermediates in protein assembly and biological regulation.

Ribosylation rapidly induces alpha-synuclein to form highly cytotoxic molten globules of advanced glycation end products

Background

Alpha synuclein (α-Syn) is the main component of Lewy bodies which are associated with several neurodegenerative diseases such as Parkinson's disease. While the glycation with D-glucose that results in α-Syn misfold and aggregation has been studied, the effects of glycation with D-ribose on α-Syn have not been investigated.

Methodology/Principal Findings

Here, we show that ribosylation induces α-Syn misfolding and generates advanced glycation end products (AGEs) which form protein molten globules with high cytotoxcity. Results from native- and SDS-PAGE showed that D-ribose reacted rapidly with α-Syn, leading to dimerization and polymerization. Trypsin digestion and sequencing analysis revealed that during ribosylation the lysinyl residues (K₅₈, K₆₀, K₈₀, K₉₆, K₉₇ and K₁₀₂) in the C-terminal region reacted more quickly with D-ribose than those of the N-terminal region. Using Western blotting, AGEs resulting from the glycation of α-Syn were observed within 24 h in the presence of D-ribose, but were not observed in the presence of D-glucose. Changes in fluorescence at 410 nm demonstrated again that AGEs were formed during early ribosylation. Changes in the secondary structure of ribosylated α-Syn were not clearly detected by CD spectrometry in studies on protein conformation. However, intrinsic fluorescence at 310 nm decreased markedly in the presence of D-ribose. Observations with atomic force microscopy showed that the surface morphology of glycated α-Syn looked like globular aggregates. thioflavin T (ThT) fluorescence increased during α-Syn incubation regardless of ribosylation. As incubation time increased, ribosylation of α-Syn resulted in a blue-shift (∼100 nm) in the fluorescence of ANS. The light scattering intensity of ribosylated α-Syn was not markedly different from native α-Syn, suggesting that ribosylated α-Syn is present as molten protein globules. Ribosylated products had a high cytotoxicity to SH-SY5Y cells, leading to LDH release and increase in the levels of reactive oxygen species (ROS).

Conclusions/Significance

α-Syn is rapidly glycated in the presence of D-ribose generating molten globule-like aggregations which cause cell oxidative stress and result in high cytotoxicity.

The human alpha-lactalbumin molten globule: comparison of structural preferences at pH 2 and pH 7

Structural investigations of molten globules provide an important contribution towards understanding protein folding pathways. A close similarity between equilibrium molten globule states and kinetic species observed during refolding has been reported for several proteins. However, the experimental conditions, and in particular the pH, under which the equilibrium and kinetic species are studied often differ significantly. For human α-lactalbumin (α-LA), the equilibrium molten globule is most often studied at pH 2, the so-called A-state, while kinetic refolding experiments are performed at neutral pH. α-LA contains a large number of acidic amino acid residues that may influence the properties of the molten globule differently at low and neutral pH. In this study, we investigate the structural preferences of the α-LA molten globule at pH 7 at the level of individual residues using nuclear magnetic resonance spectroscopy and compare these data with previous results obtained at pH 2. We show that differences exist in the conformational ensemble that describes the α-LA molten globule at these two pH values. The molten globule at pH 7 is generally less stable than that at the low pH A-state. Most notable are differences in the stability of structure for the C-helix and the calcium-binding loop that precedes it and differences in the contribution of long-range hydrophobic contacts between the N-terminal and C-terminal regions of the α-domain to the stability of the molten globule. Our results are discussed in the context of previous studies of the α-LA molten globule and can be used to reconcile apparent discrepancies in published data relating to the C-helix. In the light of our results, the low pH A-state may not be the best model for the kinetic molten globule observed during refolding of α-LA. The pH-dependent effects reported here for α-LA may be of relevance in comparisons of equilibrium and kinetic molten globules of other proteins.

Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin

Statistical theories of protein folding have long predicted plausible mechanisms for reducing the vast conformational space through distinct ensembles of structures. However, these predictions have remained untested by bulk techniques, because the conformational diversity of folding molecules has been experimentally unapproachable. Owing to recent advances in single molecule force-clamp spectroscopy, we are now able to probe the structure and dynamics of the small protein ubiquitin by measuring its length and mechanical stability during each stage of folding. Here, we discover that upon hydrophobic collapse, the protein rapidly selects a subset of minimum energy structures that are mechanically weak and essential precursors of the native fold. From this much reduced ensemble, the native state is acquired through a barrier-limited transition. Our results support the validity of statistical mechanics models in describing the folding of a small protein on biological timescales.

Kinetic analysis of urea-inactivation of beta-galactosidase in the presence of galactose

The effect of galactose on the inactivation of purified beta-galactosidase from the black bean, Kestingiella geocarpa, in 5 M urea at 50 degrees C and at pH 4.5, was determined. Lineweaver-Burk plots of initial velocity data in the presence and absence of urea and galactose were used to determine the relevant K(m) and V(max) values, with p-nitrophenyl beta-D-galactopyranoside (PNPG) as substrate, S. The inactivation data were analysed using the Tsou equation and plots. Plots of ln([P](infinity) - [P](t) ) against time in the presence of urea yielded the inactivation rate constant, A. Plots of A vs [S] at different galactose concentrations were zero order showing that A was independent of [S]. Plots of [P](infinity) vs [S] were used to determine the mode of inhibition of the enzyme by galactose, and slopes and intercepts of the 1/[P](infinity) vs. 1/[S] yielded k(+0) and k '(+0), the microscopic rate constants for the free enzyme and the enzyme-substrate complex, respectively. Plots of k(+0) and k '(+0) vs. galactose concentrations showed that galactose protected the free enzyme and not the enzyme-substrate complex against urea inactivation via a noncompetitive mechanism at low galactose concentrations and a competitive pattern of inhibition at high galactose concentrations. The implication of the different modes of inhibition in protecting the free enzyme was discussed.

Toward resolution of ambiguity for the unfolded state

The unfolded states in proteins and nucleic acids remain weakly understood despite their importance in folding processes; misfolding diseases (Parkinson's and Alzheimer's); natively unfolded proteins (as many as 30% of eukaryotic proteins, according to Fink); and the study of ribozymes. Research has been hindered by the inability to quantify the residual (native) structure present in an unfolded protein or nucleic acid. Here, a scaling model is proposed to quantify the molar degree of folding and the unfolded state. The model takes a global view of protein structure and can be applied to a number of analytic methods and to simulations. Three examples are given of application to small-angle scattering from pressure-induced unfolding of SNase, from acid-unfolded cytochrome c, and from folding of Azoarcus ribozyme. These examples quantitatively show three characteristic unfolded states for proteins, the statistical nature of a protein folding pathway, and the relationship between extent of folding and chain size during folding for charge-driven folding in RNA.

Influence of the chain stiffness on the thermodynamics of a Gō-type model for protein folding

The relative importance of local and long range interactions in the characteristics of the protein folding process has long been a matter of controversy. Computer simulations based on Gō-type models have been widely used to study this topic, but without much agreement on which type of interactions is more relevant for the foldability of a protein. In this work, the authors also employ a topology-based potential and simulation model to analyze the influence of local and long range interactions on the thermodynamics of the folding transition. The former are mainly used to control the degree of flexibility (or stiffness) of the chain, mostly appreciable in the unfolded (noncompact) state. Our results show the different effects that local and nonlocal interactions have on the entropy and the energy of the system. This implies that a balance between both types of interactions is required, so that a free energy barrier exists between the native and the denatured states. The variations in the contribution of both types of interactions have also a direct effect on the stability of the chain conformations, including the possible appearance of thermodynamic folding intermediates.

Dependence of the size of the initially collapsed form during the refolding of barstar on denaturant concentration: evidence for a continuous transition

Two-site fluorescence resonance energy transfer (FRET) measurements have been made to determine how two intra-molecular distances contract in the sub-millisecond collapse reaction that occurs initially during the refolding of the small protein barstar. FRET measurements were made on two, single-Cys and single-Trp-containing mutant forms of barstar, Cys25 and Cys62, in each of which a thionitrobenzoate (TNB) adduct was attached to the cysteine thiol. In each protein, the core tryptophan, Trp53, acted as the FRET donor, and the TNB adduct, located either at C25 or at C62, acted as the FRET acceptor. The stabilities as well as observable folding kinetics of the Cys25 and Cys62 mutant proteins were found to be identical. The presence of the TNB adduct on the cysteine did not alter the stability or folding kinetics of either protein. Thus, the FRET-monitored changes in the two labeled mutant proteins, Cys25-TNB and Cys62-TNB, could be compared directly. Refolding was commenced from unfolded protein in 8M urea, and both the Trp53 to C25-TNB distance and the Trp53 to C62-TNB distance were found to contract upon dilution of urea. The extent of contraction of each distance, which was measured at a few milliseconds of refolding, was dependent continuously on the concentration of urea present during refolding, and was different for the two distances. For either FRET pair, the gradual contraction of distance with a decrease in the concentration of urea in which refolding occurs, was continuous with the contraction of the polypeptide chain that is seen with a decrease in the concentration of urea in the range in which the protein remains completely unfolded. It therefore appears that the products of the initial sub-millisecond refolding reaction of barstar are collapsed forms, whose dimensions do not change cooperatively in an all-or-none manner, but instead, change gradually with a change in concentration of urea. Thus, the sub-millisecond polypeptide chain collapse reaction of barstar upon denaturant dilution, appears to be a continuous structural transition.

Thermodynamics of Gō-type models for protein folding

Go-type potentials, based on the inter-residue contacts present in the native structure of a protein, are frequently used to predict dynamic and structural features of the folding pathways through computer simulations. However, the mathematical form used to define the model interactions includes several arbitrary choices, whose consequences are not usually analyzed. In this work, we use a simple off-lattice protein model and a parallel tempering Monte Carlo simulation technique to carry out such analysis, centered in the thermodynamic characteristics of the folding transition. We show how the definition of a native contact has a deep impact on the presence of simple or complex transitions, with or without thermodynamic intermediates. In addition, we have checked that the width of the attractive wells has a profound effect on the free-energy barrier between the folded and unfolded states, mainly through its influence on the entropy of the denatured state.

Towards complete descriptions of the free-energy landscapes of proteins

In recent years increasingly detailed information about the structures and dynamics of protein molecules has been obtained by innovative applications of experimental techniques, in particular nuclear magnetic resonance spectroscopy and protein engineering, and theoretical methods, notably molecular dynamics simulations. In this article we discuss how such approaches can be combined by incorporating a wide range of different types of experimental data as restraints in computer simulations to provide unprecedented detail about the ensembles of structures that describe proteins in a wide variety of states from the native structure to highly unfolded species. Knowledge of these ensembles is beginning to enable the complete free-energy landscapes of individual proteins to be defined at atomic resolution. This strategy has provided new insights into the mechanism by which proteins are able to fold into their native states, or by which they fail to do so and give rise to harmful aggregates that are associated with a wide range of debilitating human diseases.