Govardhan Reddy

Role of water in protein aggregation and amyloid polymorphism.

A variety of neurodegenerative diseases are associated with amyloid plaques, which begin as soluble protein oligomers but develop into amyloid fibrils. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Mechanisms of in vivo amyloid formation involve a number of coconspirators and complex interactions with membranes. Nevertheless, understanding the biophysical basis of simpler in vitro amyloid formation is considered important for discovering ligands that preferentially bind regions harboring amyloidogenic tendencies. The determination of the fibril structure of many peptides has set the stage for probing the dynamics of oligomer formation and amyloid growth through computer simulations. Most experimental and simulation studies, however, have been interpreted largely from the perspective of proteins: the role of solvent has been relatively overlooked in oligomer formation and assembly to protofilaments and amyloid fibrils. In this Account, we provide a perspective on how interactions with water affect folding landscapes of amyloid beta (Aβ) monomers, oligomer formation in the Aβ16-22 fragment, and protofilament formation in a peptide from yeast prion Sup35. Explicit molecular dynamics simulations illustrate how water controls the self-assembly of higher order structures, providing a structural basis for understanding the kinetics of oligomer and fibril growth. Simulations show that monomers of Aβ peptides sample a number of compact conformations. The formation of aggregation-prone structures (N*) with a salt bridge, strikingly similar to the structure in the fibril, requires overcoming a high desolvation barrier. In general, sequences for which N* structures are not significantly populated are unlikely to aggregate. Oligomers and fibrils generally form in two steps. First, water is expelled from the region between peptides rich in hydrophobic residues (for example, Aβ16-22), resulting in disordered oligomers. Then the peptides align along a preferred axis to form ordered structures with anti-parallel β-strand arrangement. The rate-limiting step in the ordered assembly is the rearrangement of the peptides within a confining volume. The mechanism of protofilament formation in a polar peptide fragment from the yeast prion, in which the two sheets are packed against each other and create a dry interface, illustrates that water dramatically slows self-assembly. As the sheets approach each other, two perfectly ordered one-dimensional water wires form. They are stabilized by hydrogen bonds to the amide groups of the polar side chains, resulting in the formation of long-lived metastable structures. Release of trapped water from the pore creates a helically twisted protofilament with a dry interface. Similarly, the driving force for addition of a solvated monomer to a preformed fibril is water release; the entropy gain and favorable interpeptide hydrogen bond formation compensate for entropy loss in the peptides. We conclude by offering evidence that a two-step model, similar to that postulated for protein crystallization, must also hold for higher order amyloid structure formation starting from N*. Distinct water-laden polymorphic structures result from multiple N* structures. Water plays multifarious roles in all of these protein aggregations. In predominantly hydrophobic sequences, water accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow fibril growth rates in hydrophilic sequences.

Entropic stabilization of proteins by TMAO.

The osmolyte trimethylamine N-oxide (TMAO) accumulates in the cell in response to osmotic stress and increases the thermodynamic stability of folded proteins. To understand the mechanism of TMAO induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (leucine, L(2), serine, S(2), glutamine, Q(2), lysine, K(2), and glycine, G(2)) in order to elucidate the effect of residue-specific TMAO interactions on small fragments of solvent-exposed conformations of the denatured states of proteins. We find that TMAO preferentially hydrogen bonds with the exposed dipeptide backbone but generally not with nonpolar or polar side chains. However, interactions with the positively charged Lys are substantially greater than with the backbone. The dipeptide G(2) is a useful model of the pure amide backbone; interacts with TMAO by forming a hydrogen bond between the amide nitrogen and the oxygen in TMAO. In contrast, TMAO is depleted from the protein backbone in the hexapeptide G(6), which shows that the length of the polypeptide chain is relevant in aqueous TMAO solutions. These simulations lead to the hypothesis that TMAO-induced stabilization of proteins and peptides is a consequence of depletion of the solute from the protein surface provided intramolecular interactions are more favorable than those between TMAO and the backbone. To test our hypothesis, we performed additional simulations of the action of TMAO on an intrinsically disordered Aβ(16-22) (KLVFFAE) monomer. In the absence of TMAO, Aβ(16-22) is a disordered random coil. However, in aqueous TMAO solution, Aβ(16-22) monomer samples compact conformations. A transition from random coil to α-helical secondary structure is observed at high TMAO concentrations. The coil to α-helix transition is highly cooperative especially considering the small number of residues in Aβ(16-22). Our work highlights the potential similarities between the action of TMAO on long polypeptide chains and entropic stabilization of proteins in a crowded environment due to excluded volume interactions. In this sense, the chemical chaperone TMAO is a nanocrowding particle.

Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Aβ peptides with implications for rates of fibril formation

Recent experiments have shown that the congener Abeta(1-40)[D23-K28], in which the side chains of charged residues Asp23 and Lys28 are linked by a lactam bridge, forms amyloid fibrils that are structurally similar to the wild type (WT) Abeta peptide, but at a rate that is nearly 1000 times faster. We used all atom molecular dynamics simulations in explicit water, and two force fields, of the WT dimer, a monomer with the lactam bridge (Abeta(10-35)-lactam[D23-K28]), and the monomer and dimers with harmonically constrained D23-K28 salt bridge (Abeta(10-35)[D23-K28]) to understand the origin of the enhanced fibril rate formation. The simulations show that the assembly competent fibril-like monomer (N*) structure, which is present among the conformations sampled by the isolated monomer, with strand conformations in the residues spanning the N and C termini and a bend involving residues D(23) VGSNKG(29), are populated to a much greater extent in Abeta(10-35)[D23-K28] and Abeta(10-35)-lactam[D23-K28] than in the WT, which has negligible probability of forming N*. The salt bridge in N* of Abeta(10-35)[D23-K28], whose topology is similar to that found in the fibril, is hydrated. The reduction in the free energy barrier to fibril formation in Abeta(10-35)[D23-K28] and in Abeta(10-35)-lactam[D23-K28], compared to the WT, arises largely due to entropic restriction which enables the bend formation. A decrease in the entropy of the unfolded state and the lesser penalty for conformational rearrangement including the formation of the salt bridge in Abeta peptides with D23-K28 constraint results in a reduction in the kinetic barrier in the Abeta(1-40)-lactam[D23-K28] congener compared to the WT. The decrease in the barrier, which is related to the free energy cost of forming a bend, is estimated to be in the range (4-7)k(B)T. Although a number of factors determine the growth of fibrils, the decrease in the free energy barrier, relative to the WT, to N* formation is a major factor in the rate enhancement in the fibril formation of Abeta(1-40)[D23-K28] congener. Qualitatively similar results were obtained using simulations of Abeta(9-40) peptides and various constructs related to the Abeta(10-35) systems that were probed using OPLS and CHARMM force fields. We hypothesize that mutations or other constraints that preferentially enhance the population of the N* species would speed up aggregation rates. Conversely, ligands that lock it in the fibril-like N* structure would prevent amyloid formation.

Dynamics of locking of peptides onto growing amyloid fibrils

Sequence-dependent variations in the growth mechanism and stability of amyloid fibrils, which are implicated in a number of neurodegenerative diseases, are poorly understood. We have carried out extensive all-atom molecular dynamics simulations to monitor the structural changes that occur upon addition of random coil (RC) monomer fragments from the yeast prion Sup35 and Aβ-peptide onto a preformed fibril. Using the atomic resolution structures of the microcrystals as the starting points, we show that the RC → β-strand transition for the Sup35 fragment occurs abruptly over a very narrow time interval, whereas the acquisition of strand content is less dramatic for the hydrophobic-rich Aβ-peptide. Expulsion of water, resulting in the formation of a dry interface between 2 adjacent sheets of the Sup35 fibril, occurs in 2 stages. Ejection of a small number of discrete water molecules in the second stage follows a rapid decrease in the number of water molecules in the first stage. Stability of the Sup35 fibril is increased by a network of hydrogen bonds involving both backbone and side chains, whereas the marginal stability of the Aβ-fibrils is largely due to the formation of weak dispersion interaction between the hydrophobic side chains. The importance of the network of hydrogen bonds is further illustrated by mutational studies, which show that substitution of the Asn and Gln residues to Ala compromises the Sup35 fibril stability. Despite the similarity in the architecture of the amyloid fibrils, the growth mechanism and stability of the fibrils depend dramatically on the sequence.

Liquid state theories for the structure of water

Liquid state theories are investigated for the local structure of the simple point charge (SPC) and a modified SPC (MSPC) model of water. The latter model includes a van der Waals repulsion between the oxygen (O) and hydrogen (H) atoms, which is necessary for the implementation of some integral equation theories. Two integral equation theories, the reference interaction site model (RISM) and the diagrammatically proper Chandler–Silbey–Ladanyi (CSL) theory, are tested by comparison with simulations of the MSPC model (neither theory converges for the SPC model when the hypernetted chain closure is used). The RISM theory is in reasonable agreement with simulations, and is more accurate than the CSL theory. A density functional theory (DFT) is investigated, which treats the ideal gas functional exactly and uses a truncated expansion for the excess free energy functional. The DFT is in excellent agreement with simulations for the structure of the MSPC water model at all temperatures studied, and for the struct...

Solvent effects in polyelectrolyte adsorption: Computer simulations with explicit and implicit solvent

The adsorption of strongly charged polyelectrolyte chains to an oppositely charged planar surface is studied using computer simulation. In addition to an explicit solvent model, two implicit solvent models are considered: one where the solvent induces an implicit Lennard-Jones (ILJ) interaction between polymer sites and one where the solvent induces a many body interaction that depends on the solvent accessible surface area (SASA) of the monomers. Molecular and Brownian dynamics simulations are reported for the explicit and implicit solvent models, respectively. All three models give similar results for the adsorption of the chains in good solvent. The electrostatic attraction between the surface and the polymers is not sufficient to drive the strong adsorption that is seen in experiments. In poor solvents, the models give different results for the adsorption excess and the mechanism for polyelectrolyte adsorption. With explicit solvent, thick adsorbed layers are formed at both charged and neutral surfaces. With the SASA model, adsorbed layers are formed on the charged but not on the neutral surface. With the ILJ model, adsorbed layers are not formed on any surfaces. The results show that the solvent plays a dominant role in the adsorption of polyelectrolytes under poor solvent conditions and that many-body solvent effects have a qualitative effect on the adsorption characteristics and mechanism. In particular, SASA and depletion effects could possibly play an important role; the former can be incorporated in the SASA model, but the latter cannot. The results suggest that accurate computational models for polymer adsorption under poor solvent conditions must incorporate the solvent explicitly.

Adsorption and Dynamics of a Single Polyelectrolyte Chain near a Planar Charged Surface: Molecular Dynamics Simulations with Explicit Solvent.

The effect of solvent quality on the behavior of a polyelectrolyte chain near a charged surface is studied using molecular dynamics simulation with explicit solvent. The polyion adsorbs completely on the surface for a high enough surface charge density, and the surface charge required for complete adsorption becomes lower as the solvent quality is decreased. Several static and dynamic properties display a nonmonotonic dependence on surface charge density and solvent quality. For a given value of solvent quality the component of the radius of gyration (Rg) parallel to the surface is a nonmonotonic function of the surface charge density, and for a given surface charge density the component of Rg perpendicular to the surface is a nonmonotonic function of the solvent quality. The center-of-mass diffusion coefficient and rotational relaxation time are nonmonotonic functions of the surface charge density. Translational diffusion coefficient increases, and the rotational relaxation time decreases as solvent quality is decreased for a fixed surface charge density.

Theory of the Molecular Transfer Model for Proteins with Applications to the Folding of the src-SH3 Domain

A theoretical basis for the molecular transfer model (MTM), which takes into account the effects of denaturants by combining experimental data and molecular models for proteins, is provided. We show that the MTM is a mean field-like model that implicitly takes into account denaturant-induced many body interactions. The MTM in conjunction with the coarse-grained self organized polymer model with side chains (SOP-SC) for polypeptide chains is used to simulate the folding of the src-SH3 domain as a function of temperature (T) and guanidine hydrochloride (GdmCl) concentration [C]. Besides reproducing the thermodynamic aspects of SH3 folding, the SOP-SC also captures the cooperativity of the folding transitions. A number of experimentally testable predictions are also made. First, we predict that the melting temperature T(m)([C]) decreases linearly as [C] increases. Second, we show that the midpoints C(m,i) and melting temperatures T(m,i) at which individual residues acquire 50% of their native contacts differ from the global midpoint (C(m) ≈ 2.5 M) and melting temperature (T(m) = 355 K) at which the folded and unfolded states coexist. Dispersion in C(m,i) is greater than that found for T(m,i). Third, folding kinetics at [C] = 0 M shows that the acquisition of contacts between all the secondary structural elements and global folding occur nearly simultaneously. Finally, from the free energy profiles as a function of the structural overlap function and the radius of gyration of the protein, we find that at a fixed T the transition state moves toward the folded state as [C] increases in accord with the Hammond postulate. In contrast, we predict that along the locus of points T(m)([C]) the location of the transition state does not change. The theory and the models used here are sufficiently general for studying the folding of other single domain proteins.

The behavior of fluids near solutes: a density functional theory and computer simulation study.

The density distribution of solvent near a solute particle is studied using density functional theory and Monte Carlo simulation. The fluid atoms interact with each other via a hard sphere plus Yukawa potential, and interact with the solute via a hard sphere potential. For small solute sizes, the solvent displays liquidlike ordering near the particle. When the solute become larger, a drying transition is observed at state points near the coexistence conditions of the solvent. These predictions are similar to those of a recent theory for the hydrophobic effect by Lum, Chandler, and Weeks [J. Phys. Chem. 103, 4570 (1999)], although a comparison with simulations shows that the theory of this work is quantitatively more accurate. The connection between density functional methods and the LCW approach is also established.

Suppression of the Coffee-Ring Effect and Evaporation-Driven Disorder to Order Transition in Colloidal Droplets

The formation of a ring-like deposit at the periphery of a drying colloidal droplet is a vexing problem in many applications. We show a complete suppression of such deposits when a droplet of aqueous colloidal suspension, deposited on a glass substrate coated with a thin layer of silicone oil, is evaporated. This coating prevents the periphery of the aqueous droplet from getting pinned to the substrate and helps in suppressing the ring formation. It also decreases the surface area of the droplet, thereby decreasing the evaporation rate. These two factors together, driving the colloidal particles slowly to the center of the droplet, contribute to form an ordered crystallite at the end of the evaporation process. Brownian dynamics simulations performed to study ordering in the aggregate show that the spherical colloidal particles form face-centered cubic structures. Experiments and simulations show that slow rates of droplet evaporation and smaller-sized colloidal particles further lead to high-quality ordered colloidal crystallites.