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To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tibs.2010.03.007 Byline: Karen Rutherford (1), Valerie Daggett (1)(2) Abstract: Methyltransferases catalyze the methylation processes essential for protein/DNA repair, transcriptional regulation, and drug metabolism in vivo. More than 500 human methyltransferase polymorphisms have been identified, many of which are linked to disease. We mapped all available coding polymorphisms of seven methyltransferases onto their structures to address their structural significance, and identified a polymorphic hotspot [approximately equal to]20A from the active site in four of the proteins. Molecular dynamics simulations of these proteins reveal a common mechanism of destabilization: the mutations alter important side-chain contacts within the polymorphic site that are propagated through the protein, thereby distorting the active site. We propose that this hotspot might have arisen to modulate enzymatic activity, with decreased activity actually conferring an advantage in three of the four methyltransferases. Author Affiliation: (1) Department of Biochemistry, Box 355013, University of Washington, Seattle WA 98195-5013, USA (2) Department of Bioengineering, Box 355013, University of Washington, Seattle WA 98195-5013, USA

Here, we compare the distributions of main chain ([PHI], [PSI]) angles (i.e., Ramachandran maps) of the 20 naturally occurring amino acids in three contexts: (i) molecular dynamics (MD) simulations of GlyGly-X-Gly-Gly pentapeptides in water at 298 K with exhaustive sampling, where X = the amino acid in question; (ii) 188 independent protein simulations in water at 298 K from our Dynameomics Project; and (ii) static crystal and NMR structures from the Protein Data Bank. The GGXGG peptide series is often used as a model of the unstructured denatured state of proteins. The sampling in the peptide MD simulations is neither random nor uniform. Instead, individual amino acids show preferences for particular conformations, but the peptide is dynamic, and interconversion between conformers is facile. For a given amino acid, the ([PHI], [PSI]) distributions in the protein simulations and the Protein Data Bank are very similar and often distinct from those in the peptide simulations. Comparison between the peptide and protein simulations shows that packing constraints, solvation, and the tendency for particular amino acids to be used for specific structural motifs can overwhelm the 'intrinsic propensities' of amino acids for particular ([PHI], [PSI]) conformations. We also compare our helical propensities with experimental consensus values using the host-guest method, which appear to be determined largely by context and not necessarily the intrinsic conformational propensities of the guest residues. These simulations represent an improved coil library free from contextual effects to better model intrinsic conformational propensities and provide a detailed view of conformations making up the 'random coil' state. coil library | Dynameomics | molecular dynamics | protein folding | host-guest

The presence of a solvent-exposed alanine residue stabilizes a helix by 0.4-2 kcal * [mol.sup.-1] relative to glycine. Various factors have been suggested to account for the differences in helical propensity, from the higher conformational freedom of glycine sequences in the unfolded state to hydrophobic and van der Waals' stabilization of the alanine side chain in the helical state. We have performed all-atom molecular dynamics simulations with explicit solvent and exhaustive sampling of model peptides to address the backbone conformational entropy difference between Ala and Gly in the denatured state. The mutation of Ala to Gly leads to an increase in conformational entropy equivalent to [approximately equal to] 0.4 kcal 8 [mol.sup.-1] in a fully flexible denatured, that is, unfolded, state. But, this energy is closely counterbalanced by the (measured) difference in free energy of transfer of the glycine and alanine side chains from the vapor phase to water so that the unfolded alanineand glycine--containing peptides are approximately isoenergetic. The helix-stabilizing propensity of Ala relative to Gly thus mainly results from more favorable interactions of Ala in the folded helical structure. The small difference in energetics in the denatured states means that the [PHI]-values derived from Ala [right arrow] Gly scanning of helices are a very good measure of the extent of formation of structure in proteins with little residual structure in the denatured state. folding | pathway | protein | stability | transition state

Two fundamentally different protofibril models of misfolded prion protein are proposed and compared with the available experimental information, including electron micrographs, symmetries, secondary structure, oligomerization interfaces, enzymatic digestion, epitope exposure and disaggregation profiles. The analysis has shown that the spiral model is a plausible protofibril model and that the [beta]-helix is not.

A focus is made on molecular dynamics (MD) simulations of proteins in solution to investigate the detailed processes of protein folding and unfolding. Proteins can be expected to fairly reliably depict protein folding/unfolding transition states, intermediate states and denatured states, provided explicit solvent and good simulation techniques are employed.

Molecular dynamics simulations was used to reveal the detailed conformational behaviors of peptides and proteins and by comparing fragment and full length protein simulations, the role of each peptide segment in the folding process was investigated. The segments with different helical propensities play an important role during protein folding.

Homology models are constructed for both human catechol O-methyltransferase (COMT) polymorphs and molecular dynamics simulations of these models are performed at 25, 37 and 50 degree C to explore the structural consequences of the 108V/M polymorphism. The addition of cosubstrate S-adenosylmethionine (SAM) tightens up the cosubstrate pocket in both proteins and prevents the altered packing at the polymorphic site in 108M COMT.

The self-assembly of beta(sub 2)-microglobulin into fibrils leading to dialysis-related amyloidosis is described. It is proposed that the forming of alpha sheet facilitates self assembly into partially unfolded prefibrillar amyloidogenic intermediates.

Several neurodegenerative diseases are linked to expanded repeats of glutamine residues, which lead to the formation of amyloid fibrils and neuronal death. The length of the repeats correlates with the onset of Huntington's disease, such that healthy individuals have 38 repeats exhibit symptoms. Because it is difficult to obtain atomic-resolution structural information for poly(L-glutamine) (polyQ) in aqueous solution experimentally, we performed molecular dynamics simulations to investigate the conformational behavior of this homopolymer. In simulations of 20-, 40-, and 80-mer polyQ, we observed the formation of the '[alpha]-extended chain' conformation, which is characterized by alternating residues in the [[alpha].sub.L] and [[alpha].sub.R] conformations to yield a sheet. The structural transition from disordered random-coil conformations to the [alpha]-extended chain conformation exhibits modest length and temperature dependence, in agreement with the experimental observation that aggregation depends on length and temperature. We propose that fibril formation in polyQ may occur through an [alpha]-sheet structure, which was proposed by Pauling and Corey [Pauling, L. & Corey, R. B. (1951) Proc. Natl. Acad. Sci. USA 37, 251-256]. Also, we propose an atomic-resolution model of how the inhibitory peptide QBP1 (polyQ-binding peptide 1) may bind to polyQ in an a-extended chain conformation to inhibit fibril formation. [alpha]-sheet | amyloidosis | misfolding disease | molecular dynamics | poly(L-glutamine)

Molecular dynamics (MD) simulations are the classic single-molecule 'experiments,' providing atomic-resolution structural and dynamic information. However, the single-molecule nature of the technique has also been its shortcoming, with frequent criticisms of sampling inadequacies and questions regarding the ensemble behavior of large numbers of molecules. Given the increase in computer power, we now address this issue by performing a large number of simulations and comparing individual and ensemble properties. One hundred independent MD simulations of the protein chymotrypsin inhibitor 2 were carried out for 20 ns each at 498 K in water to more fully describe the potentially diverse routes of protein unfolding and investigate how representative a single trajectory can be. Rapid unfolding was observed in all Cases with the trajectories distributed about an average 'ensemble' path in which secondary and tertiary structure was lost concomitantly, with tertiary structure loss occurring slightly faster. Individual trajectories did, however, sample conformations far from the average path with very heterogeneous time-dependent properties. Nevertheless, all of the simulations but one followed the average ensemble pathway, such that a small number of simulations (5-10) are sufficient to capture the average properties of these states and the unfolding pathway. energy landscape | folding pathway | molecular dynamics | chymotrypsin inhibitor 2 | unfolding simulations

An assessment of three spherical atom-based cutoff approaches such as abrupt truncation, a CHARMM-style electrostatic shift truncation and a force-shift truncation for use with all-atom explicit solvent molecular dynamics (MD) is described. This work demonstrates that by using proper and rigorous techniques, it is possible to correctly model polypeptide dynamics in solution with a spherical cutoff.

High-temperature molecular dynamics simulations were used to gain insight into the early steps in the unfolding pathway of azurin, a blue copper protein with a beta-barrel structure formed by two sheets arranged in a Greek key folding topology. The results reveal that unfolding of the beta-barrel in azurin is associated with dislocation of its unique alpha-helix with respect to the protein scaffold.

The molecular dynamics (MD) simulations are employed to determine the effects of trimethylamine N-oxide (TMAO) on the dynamics and structure of the prion protein at the atomic level. It is shown that the misfolded, PrP(super Sc) -like prion protein obtained through MD simulation under the acidic conditions can be restored to a more globular structure upon addition of 1M TMAO.

Transthyretin, [[beta].sub.2]-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of [alpha]-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251-256]. In all [beta]-sheet proteins, transthyretin and [[beta].sub.2]-microglobulin, [alpha]-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, [alpha]-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of [alpha]-pleated sheet structure may be a common conformational transition in amyloidosis.

We have assessed the published predictions of the pathway of folding of the B domain of protein A, the pathway most studied by computer simulation. We analyzed the transition state for folding of the three-helix bundle protein, by using experimental [PHI] values on some 70 suitable mutants. Surprisingly, the third helix, which has the most stable [alpha]-helical structure as a peptide fragment, is poorly formed in the transition state, especially at its C terminus. The protein folds around a nearly fully formed central helix, which is stabilized by extensive hydrophobic side chain interactions. The turn connecting the poorly structured first helix to the central helix is unstructured, but the turn connecting the central helix to the third is in the process of being formed as the N-terminal region of the third helix begins to coalesce. The transition state is inconsistent with a classical framework mechanism and is closer to nucleation--condensation. None of the published atomistic simulations are fully consistent with the experimental picture although many capture important features. There is a continuing need for combining simulation with experiment to describe folding pathways, and of continued testing to improve predictive methods. [PHI] value | nucleation-condensation | framework | temperature-jump | kinetics

It is controversial whether fast-folding proteins can form productive on-pathway intermediates that are more stable than the denatured state because noncovalent intermediates are usually evanescent. Here, we apply the classical criteria for the existence of intermediates: namely, the intermediates form and react rapidly enough to be on pathway and they can be isolated and characterized. The folding of the 71-residue, mainly [alpha]-helical FF domain from human HYPA/FBP11 fulfills these classical criteria, as was found for Im7. The FF domain folds in two phases, one on the us and the other on the ms time scale. An engineered mutant folds only to a partly folded state, with some 20-40% of the native helical content, The kinetic properties of the mutant are identical to those found for the fast phase of the wild-type protein, and it is likely that the mutant folds just to the intermediate state. A full kinetic analysis of the folding of wild-type protein, using the amplitudes of its native and denatured states and the observed values for the mutant, rules out an off-pathway scheme but fits an on-pathway scheme, with a low energy intermediate that is modeled by the mutant. The experimental proof benchmarks a molecular dynamics method that identifies an obligatory intermediate observed in multiple simulations. The q space defining this intermediate is visited several times in the simulations, leading to high populations consistent with the presence of a low energy intermediate. FF domain | helix bundle | molecular dynamics | folding intermediate

Proteins are very sensitive to their solvent environments. Urea is a common chemical denaturant of proteins, yet some animals contain high concentrations of urea. These animals have evolved an interesting mechanism to counteract the effects of urea by using trimethylamine N-oxide (TMAO). The molecular basis for the ability of TMAO to act as a chemical chaperone remains unknown. Here, we describe molecular dynamics simulations of a small globular protein, chymotrypsin inhibitor 2, in 8 M urea and 4 M TMAO/8 M urea solutions, in addition to other control simulations, to investigate this effect at the atomic level. In 8 M urea, the protein unfolds, and urea acts in both a direct and indirect manner to achieve this effect. In contrast, introduction of 4 M TMAO counteracts the effect of urea and the protein remains well structured. TMAO makes few direct interactions with the protein. Instead, it prevents unfolding of the protein by structuring the solvent. In particular, TMAO orders the solvent and discourages it from competing with intraprotein H bonds and breaking up the hydrophobic core of the protein.

The ability to diagnose and treat prion diseases is limited by our current understanding of the conversion process of the protein from healthy to harmful isoform. Whereas the monomeric, benign species is well characterized, the misfolded conformations responsible for infectivity and neurodegeneration remain elusive. There is mounting evidence that fibrillization intermediates, or protofibrils, but not mature fibrils or plaques, are the pathogenic species in amyloid diseases. Here, we use molecular dynamics to simulate the conversion of the prion protein. Molecular dynamics simulation produces a scrapie prion protein-like conformation enriched in [beta]-structure that is in good agreement with available experimental data. The converted conformation was then used to model a protofibril by means of the docking of hydrophobic patches of the template structure to form hydrogen-bonded sheets spanning adjacent subunits. The resulting protofibril model provides a non-branching aggregate with a [3.sub.1] axis of symmetry that is in good agreement with a wide variety of experimental data; importantly, it was derived from realistic simulation of the conversion process.

Here, we describe the folding/unfolding kinetics of [[alpha].sub.3]D, a small designed three-helix bundle. Both IR temperature jump and ultrafast fluorescence mixing methods reveal a single-exponential process consistent with a minimal folding time of 3.2 [+ or -] 1.2 [micro]s (at [approximately equal to] 50[degrees]C), indicating that a protein can fold on the 1- to 5-[micro]s time scale. Furthermore, the single-exponential nature of the relaxation indicates that the prefactor for transition state (TS)-folding models is probably [greater than or equal to] 1 [([micro]s).sup.-1] for a protein of this size and topology. Molecular dynamics simulations and IR spectroscopy provide a molecular rationale for the rapid, single-exponential folding of this protein. [[alpha].sub.3]D shows a significant bias toward local helical structure in the thermally denatured state. The molecular dynamics-simulated TS ensemble is highly heterogeneous and dynamic, allowing access to the TS via multiple pathways.

We compare the folding of representative members of a protein superfamily by experiment and simulation to investigate common features in folding mechanisms. The homeodomain superfamily of three-helical, single-domain proteins exhibits a spectrum of folding processes that spans the complete transition from concurrent secondary and tertiary structure formation (nucleation-condensation mechanism) to sequential secondary and tertiary formation (framework mechanism). The unifying factor in their mechanisms is that the transition state for (un)folding is expanded and very native-like, with the proportion and degree of formation of secondary and tertiary interactions varying. There is a transition, or slide, from the framework to nucleation-condensation mechanism with decreasing stability of the secondary structure. Thus, framework and nucleation-condensation are different manifestations of an underlying common mechanism. two-state | three-state | framework | nucleation | homeodomain

Author(s): Ugo Mayor [1]; Nicholas R. Guydosh [1]; Christopher M. Johnson [1]; J. Günter Grossmann [2]; Satoshi Sato [1]; Gouri S. Jas [3, 4]; Stefan M. V. Freund [1]; Darwin [...]

Proteins appear to fold by diverse pathways, but variations of a simple mechanism--nucleation-condensation--describe the overall features of folding of most domains. In general, secondary structure is inherently unstable and its stability is enhanced by tertiary interactions. Consequently, an extensive interplay of secondary and tertiary interactions determines the transition-state for folding, which is structurally similar to the native state, being formed in a general collapse (condensation) around a diffuse nucleus. As the propensity for stable secondary structure increases, folding becomes more hierarchical and eventually follows a framework mechanism where the transition state is assembled from pre-formed secondary structural elements.

Research has been conducted on the proteins' all-atom molecular dynamics simulations in solvent. The analysis of these simulations which have produced the models of protein folding transition, intermediate and denatured states is presented.

The authors review the publications on protein folding events. The topic of interest include the application of the experimental and theoretical methods of protein folding at atomic level resolution and their results.

Chemical synthesis allows the incorporation of nonnatural amino acids into proteins that may provide previously untried probes of their folding pathway and thermodynamic stability. We have used a flexible thioether linker as a loop mimetic in the human yes kinase-associated protein (YAP 65) WW domain, a three-stranded, 44-residue, [beta]-sheet protein. This linkage avoids problems of incorporating sequences that constrain loops to the extent that they significantly change the nature of the denatured state with concomitant effects on the folding kinetics. An NMR solution structure shows that the thioether linker had little effect on the global fold of the domain, although the loop is apparently more dynamic. The thioether variants are destabilized by up to 1.4 kcal/mol (1 cal = 4.18 J). Preliminary [PHI]-value analysis showed that the first loop is highly structured in the folding transition state, and the second loop is essentially unstructured. These data are consistent with results from simulated unfolding and detailed protein-engineering studies of structurally homologous WW domains. Previously, [PHI]-value analysis was limited to studying side-chain interactions. The linkers used here extend the protein engineering method directly to secondary-structure interactions.

Research has been conducted on the hydrophobic deletion mutants of chymotrypsin inhibitor 2. The free energy perturbation of these mutants has been calculated via transition- and denatured-state structures from various denaturation molecular dynamics simulations.

The binding interface between cytochrome b(sub)5 and cytochrome c is investigated to understand the molecular mechanism involved in the electron-transport reactions between the cytochromes. Data show that 51% of cytochrome b(sub)5 residues exhibit chemical shift changes and these residues are localized to the binding interface.

The dynamic characteristics of the ribonuclease inhibitor barstar was studied through molecular dynamics simulations in explicit water. Results indicated that the entropy of the native state can be important and should not be neglected in thermodynamic studies of protein folding. The side chain motion shows the main source of the residual entropy of the native state and entropic studies based only on the backbone dynamics are insufficient.

Experimental data from protein engineering studies and NMR spectroscopy have been used by theoreticians to develop algorithms for helix propensity and to benchmark computer simulations of folding pathways and energy landscapes. Molecular dynamic simulations of the unfolding of chymotrypsin inhibitor 2 (CI2) have provided detailed structural models of the transition state ensemble for unfolding/folding of the protein. We now have used the simulated transition state structures to design faster folding mutants of CI2. The models pinpoint a number of unfavorable local interactions at the carboxyl terminus of the single [Alpha]-helix and in the protease-binding loop region of CI2. By removing these interactions or replacing them with stabilizing ones, we have increased the rate of folding of the protein up to 40-fold ([Tau] = 0.4 ms). This correspondence, and other examples of agreement between experiment and theory in general, [Phi]-values and molecular dynamics simulations, in particular, suggest that significant progress has been made toward describing complete folding pathways at atomic resolution by combining experiment and simulation.

Residual structure in the denatured state of a protein may contain clues about the early events in folding. We have simulated by molecular dynamics the denatured state of barnase, which has been studied by NMR spectroscopy. An ensemble of [10.sup.4] structures was generated after 2 ns of unfolding and following for a further 2 ns. The ensemble was heterogeneous, but there was nonrandom, residual structure with persistent interactions. Helical structure in the C-terminal portion of helix [Alpha]1 (residues 13-17) and in helix [Alpha]2 as well as a turn and nonnative hydrophobic clustering between [Beta]3 and [Beta]4 were observed, consistent with NMR data. In addition, there were tertiary contacts between residues in [Alpha]1 and the C-terminal portion of the [Beta]-sheet. The simulated structures allow the rudimentary NMR data to be fleshed out. The consistency between simulation and experiment inspires confidence in the methods. A description of the folding pathway of barnase from the denatured to the native state can be constructed by combining the simulation with experimental data from [Phi] value analysis and NMR.

The effect of mutations on the structure and folding properties of rat and bovine apocytochrome b5 were determined by molecular dynamics simulations. Heme removal resulted in significant changes in the structure and dynamics of the apo form compared to the native holoprotein. There were wide deviations in the experimental results for the rat apoprotein. The behavior of the two hydrophobic cores did not agree with their expected behavior. Core 1 exhibited significant conformational changes while core 2 retained its native structure.

The cytochrome b5, involved in protein-protein interactions and electron-transfer reactions, undergoes a temporary structural deviation when simulated in water at a temperature of 298K and pH 6.9, before reverting back to its original crystalline conformation.simulation detects a A region of protein backbone that changed structure consists of acidic residues, suggesting electrostatic-based protein-protein recognition. This suggests that a low-energy mechanism for controlling recognition events ay be thermal motion.

The research of modeling pH-dependent conformations of the beta (1-28) peptide by using molecular dynamics simulations is described. Molecular dynamics simulations indicate the macromolecular motion at the atomic level and reproduces the pH-dependent conformational behavior of the beta(1-28) peptide by adjusting the ionization state of the appropriate amino acid side chains. The multiconformational equilibrium of folded and unfolded species of the peptide is analyzed.

Molecular dynamics simulations needed to analyze the conformational properties of the amyloid beta (1-28) peptide were further used to evaluate the behavior of the N-terminus of the peptide. The simulations of four analogs of beta peptide containing mutations at Ser 8, Gly 9, and Glu 11 indicate the effect of a mutation on the helical state and the conformational transitions from that state.

Molecular dynamics simulations of the protein unfolding transition state of chymotrypsin inhibitor 2 show that the secondary structure is partially stable while the native tertiary contacts of the hydrophobic core are completely unstable. The ratio of the number of contacts in the residues in the native state to the number in transition state defines the degree of structural modifications in the protein. The transition state for the unfolding process from the simulations agrees with that from protein engineering techniques.

A study was done on the molten globule state using molecular dynamics simulations of protein unfolding and the resulting partially unfolded structures created from bovine pancreatic trypsin inhibitor. The partially denatured products were compact but expanded relative to the native state. The structures were mobile with the overall secondary structure contents resemblingthe native protein. There was local unfolding with the largest changes occurring in the loop regions.

Molecular dynamics of wild-type and mutated human prion proteins (PrP) are performed to understand the underlying structural and dynamic effects of these disease-causing mutations on the human PrP. The results indicated that the different effects induced by the mutations are related to misfolding of the native [beta]-sheets into different forms.

Several techniques are simultaneously employed to explain the structures and equilibrium of the hypoxia-inducible factor, HIF2[alpha] PAS-B with different artificial ligands. The various phenomenon involved in the binding of ligands in these factors are also explained.

Multiple molecular dynamics simulations of the single amino-acid substitutions R46Q, R131Q and R154H human Ogg1 are performed to predict the structural and dynamic effects of the substitutions throughout the protein and within the active site and substrate recognition site. These substitutions have not induced any unfolding or global structural changes instead their effects are confined to the active and recognition sites.

Multiple molecular dynamics simulations of the wild-type, A22S, A52T, and V108M COMT proteins were performed to explore the structural consequences of mutations in human catechol O-methyltransferase (COMT). The decreased activities of both A22S and V108M COMT associated with an increased risk for schizophrenia and the V108M-induced destabilization linked with improved cognitive function revealed that polymorphisms within this hotspot might have evolved to regulate COMT activity and might be advantageous to heterozygosity for either mutation.

Molecular dynamics (MD) simulations are performed on engrailed homeodomain (En-HD) near its melting temperature ([T.sub.m]) in order to compare unfolding and refolding under identical conditions. The studies have shown that En-HD has passed through remarkably similar unfolding and refolding transition states, but only a portion of the actual refolding pathway is similar to the unfolding pathway.

The outcomes of molecular dynamics simulations of the flexible 3-centered (F3C) water model under different conditions are presented. F3C water model reproduces properties of water in the solid phase, the supercooled liquid phase and at the ice/liquid water interface.

Molecular dynamics simulations of human histamine N-methyltransferase (HNMT) gene which contains a common threonine-isoleucine T105I are reported. Active site structure and dynamics are significantly affected by residue 105.

All-atom, explicit-solvent molecular dynamics simulations of bovine pancreatic ribonuclease A upto its melting temperature ([T.sub.m]) are presented. Subtle, functionally important changes in protein conformation take place below the [T.sub.m].

The molecular dynamics simulations of the human prion protein at low pH and at neutral pH as a control is presented. The results have shown that this prion construct is stable and native-like at neutral pH, whereas at low pH the prion protein is destabilized by disruption of critical long-range salt bridges.

Various molecular dynamics simulations are used to study the various pathways involved in the folding mechanism of proteins from a linear chain of amino acids to the three-dimensional structure with sequence identity. The results indicate that small, but highly critical sequence differences help in the determination of the topology of the protein along the folding pathway, which is very essential to study the process by which different folds are evolved.

An analysis is conducted to determine that association of conformational changes and amyloidosis results in the formation of [alpha]-sheet and it symbolizes the toxic conformer. The structural properties of the [alpha]-sheet, background information, and experimental support of this unique structure recognized through molecular dynamics simulations of different protein related with amyloid diseases under amyloidogenic conditions are described along with the role of the conformation in the diseases.

Bovine pancreatic ribonuclease (RNase A), a small monomeric protein, is investigated at very high resolutions and molecular dynamic unfolding simulations are performed at 498 K, at neutral pH and at very low pH. The results show that the same protein can have different pathways for domain swapping and in RNase A the C-terminal swapping requires a substantial unfolding of the monomers, whereas the N-terminal swapping occurs through partial unfolding.

The thermodynamics of interaction between trimethylamine n-oxide (TMAO) and protein functional groups are studied. The findings suggest that TMAO stabilizes proteins through enhancement of water structure, such that interactions with the amide unit are discouraged.

Molecular dynamics simulations with explicit waters are employed to investigate the dominant source of elastin's elasticity. The results support the hydrophobic mechanism of elasticity and provide a framework for description of the molecular basis of the phenomenon.