Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding

Dynamic protein hydration water mediates the aggregation kinetics of amyloid β peptides at interfaces

Protein hydration water is essential for protein misfolding and amyloid formation, but how it directs the course of amyloid formation has yet to be elucidated. Here, we experimentally demonstrated that femtosecond sum frequency generation vibrational spectroscopy (SFG-VS) and the femtosecond IR pump-SFG probe technique can serve as powerful tools for addressing this issue. Using amyloid β(1-42) peptide as a model, we determined the transient misfolding intermediates by probing the amide band spectral features and the local hydration water changes by measuring the ultrafast vibrational dynamics of the amide I band. For the first time, we established a correlation between the dynamic change in protein hydration water and aggregation propensity. The aggregation propensity depends on the dynamic change in the hydration water, rather than the static hydration water content of the initial protein state. Water expulsion enhances the aggregation propensity and promotes amyloid formation, while protein hydration attenuates the aggregation propensity and inhibits amyloid formation. The suppression of water expulsion and protein hydration can prevent protein aggregation and stabilize proteins. These findings contribute to a better understanding of the underlying effect of hydration water on amyloid formation and protein structural stability and provide a strategy for maintaining long-term stabilization of biomolecules.

Enhanced Hydrogen Bonding by Urea Functionalization Tunes the Stability and Biological Properties of Peptide Amphiphiles

Self-assembled nanostructures such as those formed by peptide amphiphiles (PAs) are of great interest in biological and pharmacological applications. Herein, a simple and widely applicable chemical modification, a urea motif, was included in the PA's molecular structure to stabilize the nanostructures by virtue of intermolecular hydrogen bonds. Since the amino acid residue nearest to the lipid tail is the most relevant for stability, we decided to include the urea modification at that position. We prepared four groups of molecules (13 PAs in all), with varying levels of intermolecular cohesion, using amino acids with distinct β-sheet promoting potential and/or containing hydrophobic tails of distinct lengths. Each subset contained one urea-modified PA and nonmodified PAs, all with the same peptide sequence. The varied responses of these PAs to variations in pH, temperature, counterions, and biologically related proteins were examined using microscopic, X-ray, spectrometric techniques, and molecular simulations. We found that the urea group contributes to the stabilization of the morphology and internal arrangement of the assemblies against environmental stimuli for all peptide sequences. In addition, microbiological and biological studies were performed with the cationic PAs. These assays reveal that the addition of urea linkages affects the PA-cell membrane interaction, showing the potential to increase the selectivity toward bacteria. Our data indicate that the urea motif can be used to tune the stability of a wide range of PA nanostructures, allowing flexibility on the biomaterial's design and opening a myriad of options for clinical therapies.

Biofouling-Inspired Growth of Superhydrophilic Coating of Polyacrylic Acid on Hydrophobic Surfaces for Excellent Anti-Fouling

In this work, we demonstrated effective adsorption of poly(acrylic acid) (PAA) in saline water on various hydrophobic substrates, ranging from polyethylene and polytetrafluoroethylene, to form densely packed monolayers with water contact angle as low as 6.5° in air. This was a result of the synergy of long-range hydrophobic interactions between individual PAA chains and hydrophobic surfaces and short-range hydrogen bonding between neighboring PAA chains, reminiscent of the interaction balance encountered in biofouling. The PAA monolayers adsorbed on hydrophobic surfaces showed the ultrahigh packing density of surface COOH groups of 4.8 nm^-2, which contributed to the surface superhydrophilicity and its stability against surface reconstruction during aging even at temperature higher than PAA glass transition. Further, conjugation of the adsorbed PAA monolayers with polyethylene glycol results in excellent antifouling with nearly zero adsorption of proteins.

Hydration and Dynamics of Full-Length Tau Amyloid Fibrils Investigated by Solid-State Nuclear Magnetic Resonance

The microtubule-associated protein tau aggregates into distinct neurofibrillary tangles in brains afflicted with multiple neurodegenerative diseases such as Alzheimer's disease and corticobasal degeneration (CBD). The mechanism of tau misfolding and aggregation is poorly understood. Determining the structure, dynamics, and water accessibility of tau filaments may provide insight into the pathway of tau misfolding. Here, we investigate the hydration and dynamics of the β-sheet core of heparin-fibrillized 0N4R tau using solid-state nuclear magnetic resonance spectroscopy. This β-sheet core consists of the second and third microtubule-binding repeats, R2 and R3, respectively, which form a hairpin. Water-edited two-dimensional (2D) 13C-13C and 15N-13C correlation spectra show that most residues in R2 and R3 domains have low water accessibility, indicating that this hairpin is surrounded by other proteinaceous segments. However, a small number of residues, especially S285 and S316, are well hydrated compared to other Ser and Thr residues, suggesting that there is a small water channel in the middle of the hairpin. To probe whether water accessibility correlates with protein dynamics, we measured the backbone N-H dipolar couplings of the β-sheet core. Interestingly, residues in the fourth microtubule-binding repeat, R4, show rigid-limit N-H dipolar couplings, even though this domain exhibits weaker intensities in the 2D 15N-13C correlation spectra. These results suggest that the R4 domain participates in cross-β hydrogen bonding in some of the subunits but exhibits dynamic disorder in other subunits. Taken together, these hydration and dynamics data indicate that the R2-R3 hairpin of 0N4R tau is shielded from water by other proteinaceous segments on the exterior but contains a small water pore in the interior. This structural topology has various similarities with the CBD tau fibril structure but also shows specific differences. The disorder of the R4 domain and the presence of a small water channel in the heparin-fibrillized 4R tau have implications for the structure of tau fibrils in diseased brains.

Hydration Shell of Antifreeze Proteins: Unveiling the Role of Non-Ice-Binding Surfaces

Antifreeze proteins (AFPs) have the ability to inhibit ice growth by binding to ice nuclei. Their ice-binding mechanism is still unclear, yet the hydration layer is thought to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of two AFPs and two non-AFPs. The calculated shell thickness and density of the AFPs do not feature any relevant difference with respect to the non-AFPs. Moreover, the hydration shell density is always higher than the bulk density and, thus, no low-density, ice-like layer is detected at the ice-binding surface (IBS) of AFPs. Instead, we observe local water-density differences in AFPs between the IBS (lower density) and the non-IBS (higher density). The lower solvent density at the ice-binding site can pave the way to the protein binding to ice nuclei, while the higher solvent density at the non-ice-binding surfaces might provide protection against ice growth.

Glycated Insulin Exacerbates the Cytotoxicity of Human Islet Amyloid Polypeptides: a Vicious Cycle in Type 2 Diabetes

The aggregation of human islet amyloid polypeptide (hIAPP) is one of the triggering factors of type 2 diabetes mellitus (T2DM). hIAPP is cosynthesized, costored, and cosecreted with insulin in pancreatic β-cells, and insulin inhibits hIAPP aggregation. In T2DM patients, long-term hyperglycemia causes glycation of near 10% of total insulin. The glycation not only modifies insulin but also cross-links insulin into oligomers. However, the effect of glycated human insulin on hIAPP aggregation is unknown. In this study, four physiologically relevant monosaccharides, methylglyoxal, glucose, fructose, and ribose were used to glycate human insulin and two C-terminus truncated insulin analogues. Glycated insulin monomers or low molecular weight oligomers such as dimers significantly exacerbated the cytotoxicity of hIAPP. Notably, glycation-induced cross-linking of insulin inhibited the aggregation, membrane disruption, and cytotoxicity of hIAPP, which was corroborated by a control study using EGS-induced cross-linking of insulin or lysozyme. Removal of B29^Lys on the C terminus of the insulin B chain not only abolished glycation-induced cross-linking but also attenuated the aggravation effect of glycated insulin on hIAPP cytotoxicity. Taken together, this study reveals a vicious cycle in T2DM, that hyperglycemia-driven insulin glycation exacerbates the cytotoxicity of hIAPP, which accelerates β-cells death and further deteriorates T2DM.

Molecular Order Affects Interfacial Water Structure and Temperature-Dependent Hydrophobic Interactions between Nonpolar Self-Assembled Monolayers

Understanding how material properties affect hydrophobic interactions-the water-mediated interactions that drive the association of nonpolar materials-is vital to the design of materials in contact with water. Conventionally, the magnitude of the hydrophobic interactions between extended interfaces is attributed to interfacial chemical properties, such as the amount of nonpolar solvent-exposed surface area. However, recent experiments have demonstrated that the hydrophobic interactions between uniformly nonpolar self-assembled monolayers (SAMs) also depend on molecular-level SAM order. In this work, we use atomistic molecular dynamics simulations to investigate the relationship between SAM order, water structure, and hydrophobic interactions to explain these experimental observations. The SAM-SAM hydrophobic interactions calculated from the simulations increase in magnitude as SAM order increases, matching experimental observations. We explain this trend by showing that the molecular-level order of the SAM impacts the nanoscale structure of interfacial water molecules, leading to an increase in water structure near disordered SAMs. These findings are consistent with a decrease in the solvation entropy of disordered SAMs, which is confirmed by measuring the temperature dependence of hydrophobic interactions using both simulations and experiments. This study elucidates how hydrophobic interactions can be influenced by an interfacial physical property, which may guide the design of synthetic materials with fine-tuned interfacial hydrophobicity.

Structure-based design of broadly protective group a streptococcal M protein-based vaccines

BACKGROUND

A major obstacle to the development of broadly protective M protein-based group A streptococcal (GAS) vaccines is the variability within the N-terminal epitopes that evoke potent bactericidal antibodies. The concept of M type-specific protective immune responses has recently been challenged based on the observation that multivalent M protein vaccines elicited cross-reactive bactericidal antibodies against a number of non-vaccine M types of GAS. Additionally, a new "cluster-based" typing system of 175M proteins identified a limited number of clusters containing closely related M proteins. In the current study, we used the emm cluster typing system, in combination with computational structure-based peptide modeling, as a novel approach to the design of potentially broadly protective M protein-based vaccines.

METHODS

M protein sequences (AA 16-50) from the E4 cluster containing 17 emm types of GAS were analyzed using de novo 3-D structure prediction tools and the resulting structures subjected to chemical diversity analysis to identify sequences that were the most representative of the 3-D physicochemical properties of the M peptides in the cluster. Five peptides that spanned the range of physicochemical attributes of all 17 peptides were used to formulate synthetic and recombinant vaccines. Rabbit antisera were assayed for antibodies that cross-reacted with E4 peptides and whole bacteria by ELISA and for bactericidal activity against all E4GAS.

RESULTS

The synthetic vaccine rabbit antisera reacted with all 17 E4M peptides and demonstrated bactericidal activity against 15/17 E4GAS. A recombinant hybrid vaccine containing the same E4 peptides also elicited antibodies that cross-reacted with all E4M peptides.

CONCLUSIONS

Comprehensive studies using structure-based design may result in a broadly protective M peptide vaccine that will elicit cluster-specific and emm type-specific antibody responses against the majority of clinically relevant emm types of GAS.

Folding propensity of anoplin: A molecular dynamics study of the native peptide and four mutated isoforms

Anoplin, a cationic decapeptide amide GLLKRIKTLL-NH2 derived from venom sac of the solitary wasp Anoplius samariensis has been investigated through Molecular Dynamics. The wild-type (WT) and four isoforms were simulated both in water and in the membrane-mimicking solvent trifluoroethanol (TFE). In water all the investigated species, found to be in rapid equilibrium between different conformational states, can be considered as unfolded. On the other hand, in TFE all the systems enhance their rigidity and, in general, show α-helix as the main folded conformation. Interestingly, a semi-quantitative thermodynamic analysis has suggested that the folding driving force is not always the same being in some cases (e.g., the WT Anoplin) of entropic nature and in other cases of energetic nature.

Combined effects of solvation and aggregation propensity on the final supramolecular structures adopted by hydrophobic, glycine-rich, elastin-like polypeptides

Previous work on elastin-like polypeptides (ELPs) made of hydrophobic amino acids of the type XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) has consistently shown that differing dominant supramolecular structures were formed when the suspending media were varied: helical, amyloid-like fibers when suspended in water and globules evolving into "string of bead" structures, poly(ValGlyGlyValGly), or cigar-like bundles, poly(ValGlyGlyLeuGly), when suspended in methyl alcohol. Comparative experiments with poly(LeuGlyGlyValGly) have further indicated that the interface energy plays a significant role and that solvation effects act in concomitance with the intrinsic aggregation propensity of the repeat sequence. Continuing our investigation on ELPs using surface (X-ray photoelectron spectroscopy, atomic force microscopy) and bulk (circular dichroism, Fourier transform infrared spectroscopy) techniques for their characterization, here we have compared the effect of suspending solvents (H(2)O, dimethylsulfoxide, ethylene glycol, and MeOH) on poly(ValGlyGlyValGly), the polypeptide most inclined to form long and well-refined helical fibers in water, searching for the signature of intermolecular interactions occurring between the polypeptide chains in the given suspension. The influence of sequence specificities has been studied by comparing poly(ValGlyGlyValGly) and poly(LeuGlyGlyValGly) with a similar degree of polymerization. Deposits on substrates of the polypeptides were characterized taking into account the differing evaporation rate of solvents, and tests on their stability in ultra high vacuum were performed. Finally, combining experimental and computational studies, we have revaluated the three-dimensional modeling previously proposed for the supramolecular assembly in water of poly(ValGlyGlyValGly). The results were discussed and rationalized also in the light of published data.

Protein structural and surface water rearrangement constitute major events in the earliest aggregation stages of tau

Protein aggregation plays a critical role in the pathogenesis of neurodegenerative diseases, and the mechanism of its progression is poorly understood. Here, we examine the structural and dynamic characteristics of transiently evolving protein aggregates under ambient conditions by directly probing protein surface water diffusivity, local protein segment dynamics, and interprotein packing as a function of aggregation time, along the third repeat domain and C terminus of Δtau187 spanning residues 255-441 of the longest isoform of human tau. These measurements were achieved with a set of highly sensitive magnetic resonance tools that rely on site-specific electron spin labeling of Δtau187. Within minutes of initiated aggregation, the majority of Δtau187 that is initially homogeneously hydrated undergoes structural transformations to form partially structured aggregation intermediates. This is reflected in the dispersion of surface water dynamics that is distinct around the third repeat domain, found to be embedded in an intertau interface, from that of the solvent-exposed C terminus. Over the course of hours and in a rate-limiting process, a majority of these aggregation intermediates proceed to convert into stable β-sheet structured species and maintain their stacking order without exchanging their subunits. The population of β-sheet structured species is >5% within 5 min of aggregation and gradually grows to 50-70% within the early stages of fibril formation, while they mostly anneal block-wisely to form elongated fibrils. Our findings suggest that the formation of dynamic aggregation intermediates constitutes a major event occurring in the earliest stages of tau aggregation that precedes, and likely facilitates, fibril formation and growth.

Mapping amyloid-β(16-22) nucleation pathways using fluorescence lifetime imaging microscopy

The cross-β peptide architecture is associated with numerous functional biomaterials and deleterious disease related aggregates. While these diverse and ubiquitous paracrystalline assemblies have been widely studied, a fundamental understanding of the nucleation and aggregation pathways to these structures remains elusive. Here we highlight a novel application of fluorescence lifetime imaging microscopy in characterising the critical stages of peptide aggregation. Using the central nucleating core of the amyloid-β (Aβ), Aβ(16-22), as a model cross-β system, and utilising a small fraction of rhodamine labelled peptide (Rh110-Aβ(17-22)), we map out a folding pathway from monomer to paracrystalline nanotube. Using this intrinsic fluorescence reporter, we demonstrate the effects of interfaces and evaporation on the nucleation of sub-critical concentration solutions, providing access to previously uncharacterised intermediate morphologies. Using fluorescence lifetime we follow the local peptide environment through the stages of nucleation and hydrophobic collapse, ending in a stable final structure. This work provides a metric for future implementations of measuring fluorescence lifetimes of intrinsic fluorescence reporters during the very dynamic processes relating to peptide nucleation and maturation.

Water mediation is essential to nucleation of β-turn formation in peptide folding motifs

Water-mediated bond formation: The structure of the peptide GPG-NH2 has been investigated in aqueous solution to understand the role of water in the formation of a β-turn. Using a combination of neutron diffraction enhanced by isotopic substitution, NMR spectroscopy, and computer simulations, it was found that water is an essential component to initiate folding in solution.

Turn-directed α-β conformational transition of α-syn12 peptide at different pH revealed by unbiased molecular dynamics simulations

The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn_9-6 and four hydrogen bonds (HB_9-6, HB_6-9, HB_11-4 and HB_4-11) are formed at physiological pH; turn_8-5 and five hydrogen bonds (HB_8-5, HB_5-8, HB_10-3, HB_3-10 and HB_12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn_5-2 firstly, followed by the formation of part hydrogen bonds, then turn_5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH.

Alteration of water structure by peptide clusters revealed by neutron scattering in the small-angle region (below 1 Å(-1))

Solution scattering of neutrons and x-rays can provide direct information on local interactions of importance for biomolecular folding and structure. Here, neutron scattering experiments are combined with molecular-dynamics simulation to interpret the scattering signal of a series of dipeptides with varying degrees of hydrophobicity (GlyAla, GlyPro, and AlaPro) in concentrated aqueous solution (1:20 solute/water ratio) in which the peptides form large segregates (up to 50-60 amino acids). Two main results are found: 1), the shift to lower Q of the so-called water-ring peak (Q ≈ 2 Å(-1)) arises mainly from an overlap of water-peptide and peptide-peptide correlations in the region of 1.3 <Q< 2 Å(-1), rather than from a shift of the water signal induced by the presence of the clusters; and 2), in the low-Q region (Q ≈ 0.6 Å(-1)) a positive peak is observed originating from both the solute-solute correlations and changes in the water structure induced by the formation of the clusters. In particular, the water molecules are found to be more connected than in the bulk with hydrogen-bonding directions tangential to the exposed hydrophobic surfaces, and this effect increases with increasing peptide hydrophobicity. This work demonstrates that important information on the (hydrophobic) hydration of biomolecules can be obtained in the very-small-angle region.

GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations

Molecular dynamics methodologies comprise a vital research tool for structural biology. Molecular dynamics has benefited from technological advances in computing, such as multi-core CPUs and graphics processing units (GPUs), but harnessing the full power of hybrid GPU/CPU computers remains difficult. The generalized Born/solvent-accessible surface area implicit solvent model (GB/SA) stands to benefit from hybrid GPU/CPU computers, employing the GPU for the GB calculation and the CPU for the SA calculation. Here, we explore the computational challenges facing GB/SA calculations on hybrid GPU/CPU computers and demonstrate how NAMD, a parallel molecular dynamics program, is able to efficiently utilize GPUs and CPUs simultaneously for fast GB/SA simulations. The hybrid computation principles demonstrated here are generally applicable to parallel applications employing hybrid GPU/CPU calculations.

Effects of different force fields and temperatures on the structural character of Abeta (12-28) peptide in aqueous solution

The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of Aβ (12-28) peptide in aqueous solution. Moreover, the structural character of Aβ (12-28) peptide is compared with other amyloid peptides (such as H1 and α-syn12 peptide). The two independent temperature replica exchange molecular dynamics (T-REMD) simulations were completed by using two different models (OPLS-AA/TIP4P and GROMOS 43A1/SPC). We compared the models by analyzing the distributions of backbone dihedral angles, the secondary structure propensity, the free energy surface and the formation of β-hairpin. The results show that the mostly populated conformation state is random coil for both models. The population of β-hairpin is below 8 percent for both models. However, the peptide modeled by GROMOS 43A1 form β-hairpin with turn located at residues F19-E22, while the peptide modeled by OPLS-AA form β-hairpin with turn located at residues L17-F20.

Parallel Generalized Born Implicit Solvent Calculations with NAMD

Accurate electrostatic descriptions of aqueous solvent are critical for simulation studies of bio-molecules, but the computational cost of explicit treatment of solvent is very high. A computationally more feasible alternative is a generalized Born implicit solvent description which models polar solvent as a dielectric continuum. Unfortunately, the attainable simulation speedup does not transfer to the massive parallel computers often employed for simulation of large structures. Longer cutoff distances, spatially heterogenous distribution of atoms and the necessary three-fold iteration over atom-pairs in each timestep combine to challenge efficient parallel performance of generalized Born implicit solvent algorithms. Here we report how NAMD, a parallel molecular dynamics program, meets the challenge through a unique parallelization strategy. NAMD now permits efficient simulation of large systems whose slow conformational motions benefit most from implicit solvent descriptions due to the inherent low viscosity. NAMD's implicit solvent performance is benchmarked and then illustrated in simulating the ratcheting Escherichia coli ribosome involving ~250,000 atoms.

Ion-specific weak adsorption of salts and water/octanol transfer free energy of a model amphiphilic hexapeptide

An amphiphilic hexapeptide has been used as a model to quantify how specific ion effects induced by addition of four salts tune the hydrophilic/hydrophobic balance and induce temperature-dependant coacervate formation from aqueous solution. The hexapeptide chosen is present as a dimer with low transfer energy from water to octanol. Taking sodium chloride as the reference state in the Hofmeister scale, we identify water activity effects and therefore measure the free energy of transfer from water to octanol and separately the free energy associated to the adsorption of chaotropic ions or the desorption of kosmotropic ions for the same amphiphilic peptide. These effects have the same order of magnitude: therefore, both energies of solvation as well as transfer into octanol strongly depend on the nature of the electrolytes used to formulate any buffer. Model peptides could be used on separation processes based on criteria linked to "Hofmeister" but different from volume and valency.

Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water

Water-protein interactions play a direct role in protein folding. The chain collapse that accompanies protein folding involves extrusion of water from the nonpolar core. For many proteins, including apomyoglobin (apoMb), hydrophobic interactions drive an initial collapse to an intermediate state before folding to the final structure. However, the debate continues as to whether the core of the collapsed intermediate state is hydrated and, if so, what the dynamic nature of this water is. A key challenge is that protein hydration dynamics is significantly heterogeneous, yet suitable experimental techniques for measuring hydration dynamics with site-specificity are lacking. Here, we introduce Overhauser dynamic nuclear polarization at 0.35 T via site-specific nitroxide spin labels as a unique tool to probe internal and surface protein hydration dynamics with site-specific resolution in the molten globular, native, and unfolded protein states. The (1)H NMR signal enhancement of water carries information about the local dynamics of the solvent within ∼10 Å of a spin label. EPR is used synergistically to gain insights on local polarity and mobility of the spin-labeled protein. Several buried and solvent-exposed sites of apoMb are examined, each bearing a covalently bound nitroxide spin label. We find that the nonpoloar core of the apoMb molten globule is hydrated with water bearing significant translational dynamics, only 4-6-fold slower than that of bulk water. The hydration dynamics of the native state is heterogeneous, while the acid-unfolded state bears fast-diffusing hydration water. This study provides a high-resolution glimpse at the folding-dependent nature of protein hydration dynamics.

Influence of amino acid specificities on the molecular and supramolecular organization of glycine-rich elastin-like polypeptides in water

Elastin-like polypeptides adopt complex supramolecular structures, showing either a hydrophobic or a hydrophilic surface, depending on their surrounding environment and the supporting substrate. The preferred organization is important in many situations ranging from biocompatibility to bio-function. Here we compare the n-repeat pentamer LeuGlyGlyValGly (n = 7) with the analogue ValGlyGlyValGly (n = 5), as water suspensions and as deposits on silicon substrates. These sequences contain the repeat XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) motif belonging to the hydrophobic glycine-rich domain of elastin and represent a simplified model from which to obtain information on molecular interactions functional to elastin itself. The compounds studied differ only by the presence of the -CH(2)- spacer in the Leu moiety and thus the work was aimed at revealing the influence of this spacer element on self assembly. Both polypeptides were studied under identical conditions, using combined techniques, to identify differences in their conformational states both at molecular (CD, FTIR) and supramolecular (XPS, AFM) levels. By these means, together with a Congo Red spectroscopic assay of β-sheet formation in water, a clear correlation between amino acid sequences (sequence specificity) and their kinetics and ordering of aggregation has emerged. The novel outcomes of this work are from the supplementary measurements, made to augment the AFM and XPS studies, showing that the significant step in the self assembly of both polypeptides takes place in the liquid phase and from the finding that the substitution of Val by Leu in the first position of the pentapeptide effectively inhibits the formation of amyloidal fibers.

Structural and thermodynamics characters of isolated &alpha;-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution

The structural and thermodynamics characters of α-syn12 (residues 1-12 of the human α-synuclein protein) peptide in aqueous solution were investigated through temperature replica-exchange molecular dynamics (T-REMD) simulations with the GROMOS 43A1 force field. The two independent T-REMD simulations were completed starting from an initial conformational α-helix and an irregular structure, respectively. Each replica was run for 300 ns. The structural and thermodynamics characters were studied based on parameters such as distributions of backbone dihedral angles, free energy surface, stability of folded β-hairpin structure, and favorite conformations. The results showed that the isolated α-syn12 peptide in water adopted four different conformational states: the first state was a β-hairpin ensemble with Turn(9-6) and four hydrogen bonds, the second state was a β-hairpin ensemble with two turns (Turn(9-6) and Turn(5-2)) and three hydrogen bonds, the third state was a disordered structure with both Turn(8-5) and Turn(5-2), and the last state was a π-helix ensemble. Meanwhile, we studied the free energy change of α-syn12 peptide from the unfolded state to the β-hairpin state, which was in good agreement with the experiments and molecular dynamics simulations for some other peptides. We also analyzed the driving force of the peptide transition. The results indicated that the driving forces were high solvent exposure of hydrophobic Leu8 and hydrophobic residues in secondary structure. To our knowledge, this was the first report to study the isolated α-syn12 peptide in water by T-REMD.

An improved coarse-grained model of solvation and the hydrophobic effect

We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum-Chandler-Weeks theory [J. Phys. Chem. B 134, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and 2-3 orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation, and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations.

Interplay between hydration water and headgroup dynamics in lipid bilayers

In this study, the interplay between water and lipid dynamics has been investigated by broadband dielectric spectroscopy and modulated differential scanning calorimetry (MDSC). The multilamellar lipid bilayer system 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been studied over a broad temperature range at three different water contents: about 3, 6, and 9 water molecules per lipid molecule. The results from the dielectric relaxation measurements show that at temperatures <250 K the lipid headgroup rotation is described by a super-Arrhenius temperature dependence at the lowest hydration level and by the Arrhenius law at the highest hydration level. This difference in the temperature dependence of the lipid headgroup rotation can be explained by the increasing interaction between the headgroups with decreasing water content, which causes their rotational motion to be more cooperative in character. The main water relaxation shows an anomalous dependence on the water content in the supercooled and glassy regime. In contrast to the general behavior of interfacial water, the water dynamics is fastest in the driest sample and its temperature dependence is best described by a super-Arrhenius temperature dependence. The best explanation for this anomalous behavior is that the water relaxation becomes more determined by fast local lipid motions than by the intrinsic water dynamics at low water contents. In support for this interpretation is the finding that the relaxation time of the main water process is faster than that in most other host systems at temperatures below 180 K. Thus, the dielectric relaxation data show clearly the strong interplay between water and lipid dynamics; the water influences the lipid dynamics and vice versa. In the MDSC data, we observe a weak enthalpy relaxation at 203 K for the driest sample and at 179 K for the most hydrated sample, attributed to the freezing-in of the lipid headgroup rotation observed in the dielectric data, since this motion reaches a time scale of about 100 s at about the same temperatures.

Configurational subdiffusion of peptides: a network study

Molecular dynamics (MD) simulation of linear peptides reveals configurational subdiffusion at equilibrium extending from 10⁻¹² to 10⁻⁸ s. Rouse chain and continuous-time random walk models of the subdiffusion are critically discussed. Network approaches to analyzing MD simulations are shown to reproduce the time dependence of the subdiffusive mean squared displacement, which is found to arise from the fractal-like geometry of the accessible volume in the configuration space. Convergence properties of the simulation pertaining to the subdiffusive dynamics are characterized and the effect on the subdiffusive properties of representing the solvent explicitly or implicitly is compared. Non-Markovianity and other factors limiting the range of applicability of the network models are examined.

Temperature dependence of hydrogen-bond dynamics in acetic acid-water solutions

An inelastic UV scattering experiment has been carried out on acetic acid-water solutions as a function of temperature and concentration. The analysis of experimental data indicates the presence of a crossover temperature (T(c) approximately 325 +/- 10 K). Above T(c), the energy of hydrogen bonds responsible for water-acetic acid and acetic acid-acetic acid interactions is strongly reduced. This leads to a reduction in the average number of water molecule interacting with acetic acid, as well as to a lower number of acetic acid clusters. The latter behavior can be mainly ascribed to a temperature change in the activation energy of carboxylic groups of acetic acid. These results may be also relevant to better understand the folding mechanism in protein-water solutions.

Hydration dynamics at fluorinated protein surfaces

Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions. Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of side-chain volume and fluorination on solvation dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring water molecules, slowing water motion at the protein surface.

Ab Initio Protein Folding Using a Cooperative Swarm of Molecular Dynamics Trajectories

The use of atomistic simulation techniques to directly resolve the protein tertiary structure from the primary amino acid sequence is hindered by the rough topology of the protein free energy surface and the resulting simulation time scales required. We explore here the use of a molecular dynamics technique based on swarm intelligence to identify the native states of two peptides and a Trp-cage miniprotein. In all cases, the presence of cooperative swarm interactions significantly enhanced the efficiency of molecular dynamics simulations in predicting the native conformation.

Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations

The folding of a 15-residue beta-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 micros-long for a total of 37.5 micros, are performed of the peptide in explicit solvent, at room temperature, and without the use of enhanced sampling techniques. The computed folding time of 1-1.5 micros obtained from the simulations is in good agreement with experiment [Xu, Y.; et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. A common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing. Furthermore, direct transition to the folded state from fully unstructured conformations does not take place. Instead, the peptide is always observed to form partially structured conformations involving a non-native (ESYI) turn from which the native (NPDG) turn forms, triggering the folding to the beta-hairpin.

Ligand binding and hydration in protein misfolding: insights from studies of prion and p53 tumor suppressor proteins

Protein misfolding has been implicated in a large number of diseases termed protein- folding disorders (PFDs), which include Alzheimer's disease, Parkinson's disease, transmissible spongiform encephalopathies, familial amyloid polyneuropathy, Huntington's disease, and type II diabetes. In these diseases, large quantities of incorrectly folded proteins undergo aggregation, destroying brain cells and other tissues. The interplay between ligand binding and hydration is an important component of the formation of misfolded protein species. Hydration drives various biological processes, including protein folding, ligand binding, macromolecular assembly, enzyme kinetics, and signal transduction. The changes in hydration and packing, both when proteins fold correctly or when folding goes wrong, leading to PFDs, are examined through several biochemical, biophysical, and structural approaches. Although in many cases the binding of a ligand such as a nucleic acid helps to prevent misfolding and aggregation, there are several examples in which ligands induce misfolding and assembly into amyloids. This occurs simply because the formation of structured aggregates (such as protofibrillar and fibrillar amyloids) involves decreases in hydration, formation of a hydrogen-bond network in the secondary structure, and burying of nonpolar amino acid residues, processes that also occur in the normal folding landscape. In this Account, we describe the present knowledge of the folding and misfolding of different proteins, with a detailed emphasis on mammalian prion protein (PrP) and tumoral suppressor protein p53; we also explore how ligand binding and hydration together influence the fate of the proteins. Anfinsen's paradigm that the structure of a protein is determined by its amino acid sequence is to some extent contradicted by the observation that there are two isoforms of the prion protein with the same sequence: the cellular and the misfolded isoform. The cellular isoform of PrP has a disordered N-terminal domain and a highly flexible, not-well-packed C-terminal domain, which might account for its significant hydration. When PrP binds to biological molecules, such as glycosaminoglycans and nucleic acids, the disordered segments appear to fold and become less hydrated. Formation of the PrP-nucleic acid complex seems to accelerate the conversion of the cellular form of the protein into the disease-causing isoform. For p53, binding to some ligands, including nucleic acids, would prevent misfolding of the protein. Recently, several groups have begun to analyze the folding-misfolding of the individual domains of p53, but several questions remain unanswered. We discuss the implications of these findings for understanding the productive and incorrect folding pathways of these proteins in normal physiological states and in human disease, such as prion disorders and cancer. These studies are shown to lay the groundwork for the development of new drugs.

Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains

Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20–100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient β-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events.

In studies of protein folding evidence exists for early compaction in the unfolded state, although it is unclear whether these compact conformations contain specific secondary structures (through hydrophilic interactions) or whether compaction is a non-specific hydrophobic-driven effect. Here we combine single-molecule fluorescence spectroscopy and molecular dynamics simulation to demonstrate peptide hydrogen-bond-driven polypeptide-chain collapse involving secondary structure formation as the key process in the early stage of folding. Partial structuring in unfolded polypeptide chains is shown to lead to faster contact formation kinetics than would be expected if the unfolded state were populated by featureless random-coils.

Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations

Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.