Role of hydrophobic hydration in protein stability: a 3D water-explicit protein model exhibiting cold and heat denaturation

Changes in properties of human milk under different conditions of frozen storage

Human milk is the best source of nutrition for infants. Lower freezing temperatures and faster freezing rates allow for better preservation of human milk. However, research on the freezing conditions of human milk is limited. This study investigated the effectiveness of quick freezing and suitable freezing conditions for home preservation. Human milk was stored under different freezing conditions (-18 °C, -18 °C quick freezing, -30 °C, -40 °C, -60 °C, and - 80 °C) for 30, 60, and 90 days and then evaluated for changes in the microbial counts, bioactive protein, and lipid. The results showed that the total aerobic bacterial and Bifidobacteria counts in human milk after storage at freezing temperatures of - 30 °C and lower were closer to those of fresh human milk compared to - 18 °C. Furthermore, the lysozyme loss, lipid hydrolysis degree, and volatile organic compound production were lower. However, -18 °C quick freezing storage was not markedly different from -18 °C in maintaining human milk quality. Based on the results, for household and environmental reasons, the recommended temperature for storing human milk is suggested as -30 °C.

Poly(l-alanine-co-l-threonine succinate) as a Biomimetic Cryoprotectant

We synthesized a series of [(l-Ala)x-co-(l-Thr succinate)y] (PATs), which are analogous to natural antifreezing glycoprotein with the structure of [l-Ala-l-Ala-l-Thr disaccharide]n, by varying the composition and degree of succinylation while fixing their molecular weight (Mn) and Ala/Thr ratio at approximately 10-12 kDa and 2:1, respectively. We investigated their ice recrystallization inhibition (IRI), ice nucleation inhibition (INI), dynamic ice shaping (DIS), thermal hysteresis (TH), and protein cryopreservation activities. Both IRI and INI activities were greater for PATs with higher l-Ala content (PATs-3 and PATs-4) than those with lower l-Ala content (PATs-1 and PATs-2). DIS activity with faceted crystal growth was clearly observed in PATs-2 and PATs-4 with a high degree of succinylation. TH was small with <0.1 °C for all PATs and slightly greater for PATs with a high l-Ala content. Except for PATs-1, the protein (lactate dehydrogenase, LDH) stabilization activity was excellent for all PATs studied, maintaining LDH activity as high as that of fresh LDH even after 15 freeze-thaw cycles. To conclude, the cryo-active biomimetic PATs were synthesized by controlling the l-Ala content and degree of succinylation. Our results showed that PATs with an l-Ala content of 65-70% and degree of succinylation of 12-19% exhibited the cryo-activities of IRI, INI, and DIS, and particularly promising properties for the cryoprotection of LDH protein.

Application of Formulation Principles to Stability Issues Encountered During Processing, Manufacturing, and Storage of Drug Substance and Drug Product Protein Therapeutics

The field of formulation and stabilization of protein therapeutics has become rather extensive. However, most of the focus has been on stabilization of the final drug product. Yet, proteins experience stress and degradation through the manufacturing process, starting with fermentaition. This review describes how formulation principles can be applied to stabilize biopharmaceutical proteins during bioprocessing and manufacturing, considering each unit operation involved in prepration of the drug substance. In addition, the impact of the container on stabilty is discussed as well.

Effect of Chemical Chaperones on the Stability of Proteins during Heat- or Freeze-Thaw Stress

The importance of studying the structural stability of proteins is determined by the structure-function relationship. Protein stability is influenced by many factors among which are freeze-thaw and thermal stresses. The effect of trehalose, betaine, sorbitol and 2-hydroxypropyl-β-cyclodextrin (HPCD) on the stability and aggregation of bovine liver glutamate dehydrogenase (GDH) upon heating at 50 °C or freeze-thawing was studied by dynamic light scattering, differential scanning calorimetry, analytical ultracentrifugation and circular dichroism spectroscopy. A freeze-thaw cycle resulted in the complete loss of the secondary and tertiary structure, and aggregation of GDH. All the cosolutes suppressed freeze-thaw- and heat-induced aggregation of GDH and increased the protein thermal stability. The effective concentrations of the cosolutes during freeze-thawing were lower than during heating. Sorbitol exhibited the highest anti-aggregation activity under freeze-thaw stress, whereas the most effective agents stabilizing the tertiary structure of GDH were HPCD and betaine. HPCD and trehalose were the most effective agents suppressing GDH thermal aggregation. All the chemical chaperones stabilized various soluble oligomeric forms of GDH against both types of stress. The data on GDH were compared with the effects of the same cosolutes on glycogen phosphorylase b during thermal and freeze-thaw-induced aggregation. This research can find further application in biotechnology and pharmaceutics.

Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage

The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.

Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage

The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP), and Stoichiometry of GroEL-GroES Complexes

Chaperonins are nanomachines that harness ATP hydrolysis to power and catalyze protein folding, a chemical action that is directly linked to the maintenance of cell function through protein folding/refolding and assembly. GroEL and the GroEL-GroES complex are archetypal examples of such protein folding machines. Here, variable-temperature electrospray ionization (vT-ESI) native mass spectrometry is used to delineate the effects of solution temperature and ATP concentrations on the stabilities of GroEL and GroEL-GroES complexes. The results show clear evidence for destabilization of both GroEL₁₄ and GroES₇ at temperatures of 50 and 45 °C, respectively, substantially below the previously reported melting temperature (T_m ∼ 70 °C). This destabilization is accompanied by temperature-dependent reaction products that have previously unreported stoichiometries, viz. GroEL₁₄-GroES_y-ATP_n, where y = 1, 2, 8 and n = 0, 1, 2, 8, that are also dependent on Mg²⁺ and ATP concentrations. Variable-temperature native mass spectrometry reveals new insights about the stability of GroEL in response to temperature effects: (i) temperature-dependent ATP binding to GroEL; (ii) effects of temperature as well as Mg²⁺ and ATP concentrations on the stoichiometry of the GroEL-GroES complex, with Mg²⁺ showing greater effects compared to ATP; and (iii) a change in the temperature-dependent stoichiometries of the GroEL-GroES complex (GroEL₁₄-GroES₇ vs GroEL₁₄-GroES₈) between 24 and 40 °C. The similarities between results obtained by using native MS and cryo-EM [Clare et al. An expanded protein folding cage in the GroEL-gp31 complex. J. Mol. Biol. 2006, 358, 905-911; Ranson et al. Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.Nat. Struct. Mol. Biol. 2006, 13, 147-152] underscore the utility of native MS for investigations of molecular machines as well as identification of key intermediates involved in the chaperonin-assisted protein folding cycle.

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.

Design of an Ice Recrystallization-Inhibiting Polyampholyte-Containing Graft Polymer for Inhibition of Protein Aggregation

Freezing-induced damage to proteins, through osmotic stress and ice recrystallization, during protein processing and long-term storage is a serious concern and may lead to loss of protein activity owing to denaturation. In this study, graft copolymers composed of a cryoprotective polymer (capable of preventing osmotic stress) and poly(vinyl alcohol) (PVA; known for its high ice recrystallization inhibition (IRI) property) were developed. The polymers had high IRI activity, albeit slightly lower than that of PVA alone, but substantially higher than that of succinylated ε-poly-l-lysine (PLLSA) alone. The graft polymers showed an efficiency higher than that of PVA or PLLSA alone in protecting proteins from multiple freeze-thaw cycles, as well as during prolonged freezing, indicating a synergy between PVA and PLLSA. The PLLSA-based graft polymer is a promising material for use in protein biopharmaceutics for the long-term storage of proteins under freezing conditions.

In Situ Monitoring of Protein Unfolding/Structural States under Cold High-Pressure Stress

Biopharmaceutical formulations may be compromised by freezing, which has been attributed to protein conformational changes at a low temperature, and adsorption to ice-liquid interfaces. However, direct measurements of unfolding/conformational changes in sub-0 °C environments are limited because at ambient pressure, freezing of water can occur, which limits the applicability of otherwise commonly used analytical techniques without specifically tailored instrumentation. In this report, small-angle neutron scattering (SANS) and intrinsic fluorescence (FL) were used to provide in situ analysis of protein tertiary structure/folding at temperatures as low as -15 °C utilizing a high-pressure (HP) environment (up to 3 kbar) that prevents water from freezing. The results show that the α-chymotrypsinogen A (aCgn) structure is reasonably maintained under acidic pH (and corresponding pD) for all conditions of pressure and temperature tested. On the other hand, reversible structural changes and formation of oligomeric species were detected near -10 °C via HP-SANS for ovalbumin under neutral pD conditions. This was found to be related to the proximity of the temperature of cold denaturation of ovalbumin (T_CD ∼ -17 °C; calculated via isothermal chemical denaturation and Gibbs-Helmholtz extrapolation) rather than a pressure effect. Significant structural changes were also observed for a monoclonal antibody, anti-streptavidin IgG1 (AS-IgG1), under acidic conditions near -5 °C and a pressure of ∼2 kbar. The conformational perturbation detected for AS-IgG1 is proposed to be consistent with the formation of unfolding intermediates such as molten globule states. Overall, the in situ approaches described here offer a means to characterize the conformational stability of biopharmaceuticals and proteins more generally under cold-temperature stress by the assessment of structural alteration, self-association, and reversibility of each process. This offers an alternative to current ex situ methods that are based on higher temperatures and subsequent extrapolation of the data and interpretations to the cold-temperature regime.

Changes in bioactive proteins and serum proteome of human milk under different frozen storage

This study aimed to investigate changes in macronutrients, total bacterial count, and serum proteome of human milk (HM) under different frozen storage (-18°C and -60°C, 60 d and 180 d) by using IBT Labeling proteomics techniques and ELISA kit. The results indicated that total protein concentrations and total aerobic bacterial counts were significantly decreased at -18°C, while no difference at -60°C. A total of 1617 proteins were identified and quantified, and 173 proteins were significantly different. The -18°C storage had much higher influence on HM serum protein profiles than that of -60°C. Increased milk fat globule membrane (MFGM) proteins at -18°C are highly related to the damage of MFGM and transfer of MFGM proteins. The reduction of bioactive proteins is probably related to the ice-induced denaturation. In conclusion, fast cooling and ultra-low constant temperature are more suitable for the cryopreservation of human milk.

A model-based approach for the rational design of the freeze-thawing of a protein-based formulation

Proteins are unstable molecules that may be severely injured by stresses encountered during freeze-thawing. Despite this, the selection of freeze-thaw conditions is currently empirical, and this results in reduced process control. Here we propose a mathematical model that takes into account the leading causes of protein instability during freeze-thawing, i.e. cold denaturation and surface-induced unfolding, and may guide the selection of optimal operating conditions. It is observed that a high cooling rate is beneficial for molecules that are extremely sensitive to cold denaturation, while the opposite is true when ice-induced unfolding is dominant. In all cases, a fast thawing rate is observed to be beneficial. The simulation outputs are confirmed by experimental data for myoglobin and lactate dehydrogenase, suggesting that the proposed modeling approach can reproduce the main features of protein behavior during freeze-thawing. This approach can therefore guide the selection of optimal conditions for protein-based formulations that are stored in a frozen or freeze-dried state.

Considerations on Protein Stability During Freezing and Its Impact on the Freeze-Drying Cycle: A Design Space Approach

Freezing is widely used during the manufacturing process of protein-based therapeutics, but it may result in undesired loss of biological activity. Many variables come into play during freezing that could adversely affect protein stability, creating a complex landscape of interrelated effects. The current approach to the selection of freezing conditions is however nonsystematic, resulting in poor process control. Here we show how mathematical models, and a design space approach, can guide the selection of the optimal freezing protocol, focusing on protein stability. Two opposite scenarios are identified, suggesting that the ice-water interface is the dominant cause of denaturation for proteins with high bulk stability, while the duration of the freezing process itself is the key parameter to be controlled for proteins that are susceptible to cold denaturation. Experimental data for lactate dehydrogenase and myoglobin as model proteins support the model results, with a slow freezing rate being optimal for lactate dehydrogenase and the opposite being true for myoglobin. A possible application of the calculated design space to the freezing and freeze-drying of biopharmaceuticals is finally described, and some considerations on process efficiency are discussed as well.

The Cold Thermal Response of an Amyloid Oligomer Differs from Typical Globular Protein Cold Denaturation

In contrast with the general behavior of folded proteins, the cold thermal response of amyloid assemblies is difficult to elicit with simple models. We exploit exhaustive simulations to evaluate the thermal response of a barrel-shaped model amyloid oligomer, with a distinct hydrophobic core akin to that of folded proteins. Cumulative thermal data over the range of 210-483 K indicate a sharp inflection and rise in structural stability as the temperature is decreased below the melting temperature of the water model. This is not commensurate with the equilibrium free energy profile obtained with core packing as the order parameter. However, energetic analyses and the size of their fluctuations indicate the crucial role of hydration in mediating structural transitions, beyond the expected temperature-dependent hydrophobic effect. Structural ordering of the hydration layer over bulk water is maximized at the transition and vanishes at high temperatures. This is a first direct demonstration of the microscopic influence of hydration water on the low-temperature response of an amyloid assembly close to the cryo-regime.

Computational Investigation of the Effect of Pressure on Protein Stability

Previous studies show parabolic or elliptical regions of protein stability in the pressure-temperature ( P, T) plane. The construction of stability diagrams requires accessing a sufficiently broad ( P, T) range, which is often frustrated by ice formation in experiments and sampling challenges in simulations. We perform a fully atomistic computational study of the miniprotein Trp-cage over the range of temperatures 210 ≤ T ≤ 420 K and pressures P ≤ 5 kbar and construct the corresponding stability diagram. At ambient temperature, pressure shifts the conformational states toward unfolding. Below 250 K, the native fold's stability depends nonmonotonically on pressure. While cold unfolding and thermal denaturation differ significantly at ambient pressure, they exhibit progressive similarity at elevated pressures. At ambient pressure, cold denaturation is an enthalpically driven process that preserves significant elements of Trp-cage's secondary structure. In contrast, cold unfolding at elevated pressures involves a more substantial loss of secondary and tertiary structure, similar to thermal denaturation.

Comparative Study of the Effects of Temperature and Pressure on the Water-Mediated Interactions between Apolar Nanoscale Solutes

We perform molecular dynamics simulations to study the effects of temperature and pressure on the water-mediated interaction (WMI) between two nanoscale (apolar) graphene plates at 240 ≤ T ≤ 400 K and -100 ≤ P ≤ 1200 MPa. These are thermodynamic conditions relevant to, for example, cooling-, heating-, compression-, and decompression-induced protein denaturation. We find that at all ( T, P) studied, the potential of mean force between the graphene plates, as a function of plate separation r, exhibits local minima at specific plate separations r = r _n that can accommodate n water layers ( n = 0,1,2,3). In particular, our results show that isobaric cooling and isothermal compression have a similar effect on WMI between the plates; both processes tend to suppress the attraction and ultimate collapse of the graphene plates by kinetically trapping the plates at the metastable states with r = r _n ( n > 0). In addition, isobaric heating and isothermal decompression also have a similar effect; both processes tend to reduce the range and strength of the interactions between the graphene plates. Interestingly, at low temperatures, the WMI between the plates is affected by crystallization. However, crystallization depends deeply on the water model considered, SPC/E and TIP4P/2005 water models, with the crystallization occurring at different ( T, P) conditions, into different forms of ice.

Computational investigation of cold denaturation in the Trp-cage miniprotein

The functional native states of globular proteins become unstable at low temperatures, resulting in cold unfolding and impairment of normal biological function. Fundamental understanding of this phenomenon is essential to rationalizing the evolution of freeze-tolerant organisms and developing improved strategies for long-term preservation of biological materials. We present fully atomistic simulations of cold denaturation of an α-helical protein, the widely studied Trp-cage miniprotein. In contrast to the significant destabilization of the folded structure at high temperatures, Trp-cage cold denatures at 210 K into a compact, partially folded state; major elements of the secondary structure, including the α-helix, are conserved, but the salt bridge between aspartic acid and arginine is lost. The stability of Trp-cage's α-helix at low temperatures suggests a possible evolutionary explanation for the prevalence of such structures in antifreeze peptides produced by cold-weather species, such as Arctic char. Although the 310-helix is observed at cold conditions, its position is shifted toward Trp-cage's C-terminus. This shift is accompanied by intrusion of water into Trp-cage's interior and the hydration of buried hydrophobic residues. However, our calculations also show that the dominant contribution to the favorable energetics of low-temperature unfolding of Trp-cage comes from the hydration of hydrophilic residues.

Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study

We investigate, using atomistic molecular dynamics simulations, the association of surface hydration accompanying local unfolding in the mesophilic protein Yfh1 under a series of thermal conditions spanning its cold and heat denaturation temperatures. The results are benchmarked against the thermally stable protein, Ubq, and behavior at the maximum stability temperature. Local unfolding in Yfh1, predominantly in the beta sheet regions, is in qualitative agreement with recent solution NMR studies; the corresponding Ubq unfolding is not observed. Interestingly, all domains, except for the beta sheet domains of Yfh1, show increased effective surface hydrophobicity with increase in temperature, as reflected by the density fluctuations of the hydration layer. Velocity autocorrelation functions (VACF) of oxygen atoms of water within the hydration layers and the corresponding vibrational density of states (VDOS) are used to characterize alteration in dynamical behavior accompanying the temperature dependent local unfolding. Enhanced caging effects accompanying transverse oscillations of the water molecules are found to occur with the increase in temperature preferentially for the beta sheet domains of Yfh1. Helical domains of both proteins exhibit similar trends in VDOS with changes in temperature. This work demonstrates the existence of key signatures of the local onset of protein thermal denaturation in solvent dynamical behavior.

Contribution of Water to Pressure and Cold Denaturation of Proteins

The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.

A fully atomistic computer simulation study of cold denaturation of a β-hairpin

Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in molecular details can provide a new insight into the detailed natures of hydrophobic forces governing the stability of proteins in water. We show that the cold-denaturation-like phenomenon can be directly observed at low temperatures using a fully atomistic molecular dynamics simulation method. Using a highly optimized protein force field in conjunction with three different explicit water models, a replica exchange molecular dynamics simulation scheme at constant pressures allows for the computation of the melting profile of an experimentally well-characterized β-hairpin peptide. For all three water models tested, the simulated melting profiles are indicative of possible cold denaturation. From the analysis of simulation ensembles, we find that the most probable cold-denatured structure is structurally compact, with its hydrogen bonds and native hydrophobic packing substantially disrupted.

The non-uniform early structural response of globular proteins to cold denaturing conditions: a case study with Yfh1

The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at Tc in comparison to Ts. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at Tc. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.

Temperature-dependent solvation modulates the dimensions of disordered proteins

For disordered proteins, the dimensions of the chain are an important property that is sensitive to environmental conditions. We have used single-molecule Förster resonance energy transfer to probe the temperature-induced chain collapse of five unfolded or intrinsically disordered proteins. Because this behavior is sensitive to the details of intrachain and chain-solvent interactions, the collapse allows us to probe the physical interactions governing the dimensions of disordered proteins. We find that each of the proteins undergoes a collapse with increasing temperature, with the most hydrophobic one, λ-repressor, undergoing a reexpansion at the highest temperatures. Although such a collapse might be expected due to the temperature dependence of the classical "hydrophobic effect," remarkably we find that the largest collapse occurs for the most hydrophilic, charged sequences. Using a combination of theory and simulation, we show that this result can be rationalized in terms of the temperature-dependent solvation free energies of the constituent amino acids, with the solvation properties of the most hydrophilic residues playing a large part in determining the collapse.

Unified description of solvent effects in the helix-coil transition

We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background in vacuo Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be explicitly and exactly traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of intrinsically disordered proteins and their analogues.

Single-molecule spectroscopy of cold denaturation and the temperature-induced collapse of unfolded proteins

Recent Förster resonance energy transfer (FRET) experiments show that heat-unfolded states of proteins become more compact with increasing temperature. At the same time, NMR results indicate that cold-denatured proteins are more expanded than heat-denatured proteins. To clarify the connection between these observations, we investigated the unfolded state of yeast frataxin, whose cold denaturation occurs at temperatures above 273 K, with single-molecule FRET. This method allows the unfolded state dimensions to be probed not only in the cold- and heat-denatured range but also in between, i.e., in the presence of folded protein, and can thus be used to link the two regimes directly. The results show a continuous compaction of unfolded frataxin from 274 to 320 K, with a slight re-expansion at higher temperatures. Cold- and heat-denatured states are thus essentially two sides of the same coin, and their behavior can be understood within the framework of the overall temperature dependence of the unfolded state dimensions.

Effects of sequence and solvation on the temperature-pressure conformational landscape of proteinlike heteropolymers

We study the role of sequence and solvation in shaping the temperature-pressure (T, P) conformational landscape of model heteropolymers with a coarse-grained model. We design foldable primarily hydrophobic sequences with fixed polar content in water at physiological conditions, which demonstrate (T, P) dependence of conformational stability similar to biological proteins. Inherent helicity emerges as a result of local polar-polar interactions in the sequences that mimic biological α helices. The helical propensity is reduced upon solvation and remains unaltered at cold T and high P, which is driven by the T-P induced changes of the hydration shell. Consequently, at nonphysiological conditions the weakening of hydrophobic interactions facilitates population of non-native, helical, compact conformations stabilized through direct nonlocal interactions between polar residues.

Effect of osmolytes on the fibrillation of HypF-N

We have studied the effect of a series of stabilizing and destabilizing osmolytes on the fibrillation pattern of a model amyloidogenic protein, HypF-N. Under mildly denaturing conditions, HypF-N forms cross β-sheet structures, characteristic of amyloid fibrils. In the presence of all stabilizing osmolytes except proline, fibrillation of HypF-N is inhibited. Notably, fibrillation kinetics is retarded at subdenaturing concentrations of chaotropes. In case of proline, fibrillation of HypF-N is accelerated. Thus, the changes during exposure of a protein to denaturing conditions in the presence of osmolyes cannot be extrapolated from their role as anti-fibrillation agents.

Picosecond-resolved solvent reorganization and energy transfer in biological and model cavities

Water molecules in hydrophobic biological cleft/cavities are of contemporary interest for the biomolecular structure and molecular recognition of hydrophobic ligands/drugs. Here, we have explored picosecond-resolved solvation dynamics of water molecules and associated polar amino acids in the hydrophobic cleft around Cys-34 position of Endogenous Serum Albumin (ESA). While site selective acrylodan labeling to Cys-34 allows us to probe solvation in the cleft, Förster resonance energy transfer (FRET) from intrinsic fluorescent amino acid Trp 214 to the extrinsic acrylodan probes structural integrity of the protein in our experimental condition. Temperature dependent solvation in the cleft clearly shows that the dynamics follows Arrhenius type behavior up to 60 °C, after which a major structural perturbation of the protein is evident. We have also monitored polarization gated dynamics of the acrylodan probe and FRET from Trp 214 to acrylodan at various temperatures. The dynamical behavior of the immediate environments around the probe acrylodan in the cleft has been compared with a model biomimetic cavity of a reverse micelle (w0 = 5). Using same fluorescent probe of acrylodan, we have checked the structural integrity of the model cavity at various temperatures using picosecond-resolved FRET from Trp to acrylodan in the cavity. We have also estimated possible distribution of donor-acceptor distances in the protein and reverse micelles. Our studies reveal that the energetics of the water molecules in the biological cleft is comparable to that in the model cavity indicating a transition from bound state to quasibound state, closely consistent with a recent MD simulation study.

DPD Simulation of Protein Conformations: From α-Helices to β-Structures

We suggest a coarse-grained model for DPD simulations of polypeptides in solutions. The model mimics hydrogen bonding that stabilizes α-helical and β-structures using dissociable Morse bonds between quasiparticles representing the peptide groups amenable to hydrogen bonding. We demonstrate the capabilities of the model by simulating transitions between coil-like, globular, α-helical, and β-hairpin configurations of model peptides, varying Morse potential parameters, the hydrophobicities of residue side chains, and pH, which determines the charges of residue side chains. We construct a model triblock polypeptide mimicking the sequence of residues α-synuclein at two different pHs. The conformations of this model polypeptide depend on pH similarly to the behavior observed experimentally. The suggested approach to accounting for hydrogen bond formation within the general DPD framework may make the DPD method a competitive alternative to CGMD for modeling equilibrium and dynamic properties of proteins and polypeptides, especially during their transport in confined environments.

Thermal stability of hydrophobic helical oligomers: a lattice simulation study in explicit water

We investigate the thermal stability of helical hydrophobic oligomers using a three-dimensional, water-explicit lattice model and the Wang-Landau Monte Carlo method. The degree of oligomer helicity is controlled by the parameter ε(mm) < 0, which mimics monomer-monomer hydrogen bond interactions leading to the formation of helical turns in atomistic proteins. We vary |ε(mm)| between 0 and 4.5 kcal/mol and therefore investigate systems ranging from flexible homopolymers (i.e., those with no secondary structure) to helical oligomers that are stable over a broad range of temperatures. We find that systems with |ε(mm)| ≤ 2.0 kcal/mol exhibit a broad thermal unfolding transition at high temperature, leading to an ensemble of random coils. In contrast, the structure of conformations involved in a second, low-temperature, transition is strongly dependent on |ε(mm)|. Weakly helical oligomers are observed when |ε(mm)| ≤ 1.0 kcal/mol and exhibit a low-temperature, cold-unfolding-like transition to an ensemble of strongly water-penetrated globular conformations. For higher |ε(mm)| (1.7 kcal/mol ≤ |ε(mm)| ≤ 2.0 kcal/mol), cold unfolding is suppressed, and the low-temperature conformational transition becomes a "crystallization", in which a "molten" helix is transformed into a defect-free helix. The molten helix preserves ≥50% of the helical contacts observed in the "crystal" at a lower temperature. When |ε(mm)| = 4.5 kcal/mol, we find that conformational transitions are largely suppressed within the range of temperatures investigated.