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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.

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.

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.

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.

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 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.

The atomic interactions resulting from the addition of trans-sodium crocetinate (TSC) were analyzed to explain the diffusion of oxygen through aqueous solutions. The diffusivity levels of oxygen which were recorded at 3-5 Angstrom from TSC within the shell were larger than the bulk value. Moreover, hydrophobic hydration established an orderly channel which facilitated the efficient diffusion of oxygen in aqueous solutions.

A study conducted on the heme-containing protein, cytochrome b5, introduced mutations in the protein in an attempt to alter and thereby test cleft formation. Computer modeling and mutagenesis were used to design and produce two cytochrome b5 mutants, an S18D mutant and a disulfide mutant, that would restrict the cleft fluctuations. The effects of the mutations on equilibrium stability were also investigated experimentally. Results are discussed.

A study on the hemoprotein cytochrome b5 was conducted to test previous experimental results which had indicated that the molecule is highly dynamic in solution and has redox-state-dependent differences in mobility near the cleft region. Site-directed mutants aimed at perturbing cleft dynamics were constructed with a disulfide or salt bridge. Equilibrium denaturation investigations were performed while experimental methods and results were also discussed.

Molecular dynamics simulations of thermal denaturation of wild-type and two mutant forms of barnase are employed in the comparison of the phi-value analysis of the folding/unfolding pathway of barnase with an explicit structural analysis of the transition state. Results of experiment and simulation were searched for similarities, finding excellent agreement. THe key difference between simulation and experiment is the presence of alpha2 in the simulated transition state, although phi-values indicate that it is unstructured.

Molecular dynamics (MD) is the only technique availablefor obtainingdynamic protein data at atomic spatial resolution and picosecond orfiner temporal resolution. In recent years, the cost of computationalresources has decreased exponentially while the number of known proteinstructures, many of which are not characterized biochemically, hasincreased rapidly. These events have led to an increase in the useof MD in biological research, both to examine phenomena that cannotbe resolved experimentally and to generate hypotheses that directfurther experimental research. In fact, several databases of MD simulationshave arisen in recent years. MD simulations, and especially MD simulationdatabases, contain massive amounts of data, yet interesting phenomenaoften occur over very short time periods and on the scale of onlya few atoms. Analysis of such data must balance these fine-detailevents with the global picture they create. Here, we address the multiscalenature of the problem by comparing several MD analysis methods toshow their strengths and weaknesses at various scales using the wild-typeand R282W mutant forms of the DNA-binding domain of protein p53. Byleveraging these techniques together, we are able to pinpoint fine-detailand big picture differences between the protein’s variants.Our analyses indicate that the R282W mutation of p53 destabilizesthe L1 loop and loosens the H2 helix conformation, but the loosenedL1 loop can be rescued by residue H115, preventing the R282W mutationfrom completely destabilizing the protein or abolishing activity. [ABSTRACT FROM AUTHOR]

The p53 tumor suppressor is a transcription factor involved in many important signaling pathways, such as apoptosis and cell-cycle arrest. In over half of human cancers, p53 function is compromised by a mutation in its gene. Mutations in the p53 DNA-binding core domain destabilize the structure and reduce DNA.binding activity. We performed molecular dynamics simulations at physiological temperature to study the structural and dynamic effects of the L145Q V157F, and R282W cancer-associated mutations in comparison to the wild-type protein. While there were common regions of destabilization in the mutant simulations, structural changes particular to individual mutations were also observed. Significant backbone deviations of the H2 helix and S7-S8 loop were observed in all mutant simulations; the H2 helix binds to DNA In addition, the L14SQ and V1S7F mutations, which are located in the β-sandwich core of the domain, disrupted the β-sheet structure and the loop-sheet-helix motif The R282W mutation caused distortion of the loop-sheet-helix motif but otherwise this mutant was similar to the wild-type structure. The introduction of these mutations caused rearrangement of the DNA-binding surface, consistent with their reduced DNA-binding activity. The simulations reveal detailed effects of the mutations on the stability and dynamics of p53 that may provide insight for therapeutic approaches. [ABSTRACT FROM AUTHOR]

The problem of how a protein folds from a linear chain of amino acids to the three-dimensional structure necessary for function is often investigated using proteins with a low degree of sequence identity that adopt different folds. The design of pairs of proteins with a high degree of sequence identity but different folds offers the opportunity for a complementary study; in two highly similar sequences, which residues are the most important in directing folding to a particular structure? Here we use molecular dynamics simulations to characterize the folding-unfolding pathways of a pair of proteins designed by Bryan and co-workers [Alexander, P. A., et al. (2005) Biochemistry 44, 14045-14054; He, Y. N., et al. (2005) Biochemistry 44, 14055-14061]. Despite being 59% identical, the two protein sequences fold to two different structures. The first sequence folds to the α+β protein G structure and the second to the all-α-helical protein A structure. We show that the final protein structure is determined early along the folding pathway. In folding to the protein G structure, the single α-helix (α1) and the β3-β4 turn fold early. Formation of the hairpin turn essentially prevents folding to helical structure in this region of the protein. This early structure is then consolidated by formation of long-range hydrophobic interactions between al and the β3-β4 turn. The protein A sequence differs both in the residues that form the β3-β4 turn and also in many of the residues that form the early hydrophobic interactions in the protein G structure. Instead, in the protein A sequence, a more hierarchical mechanism is observed, with helices folding before many of the tertiary interactions are formed. We find that small, but critical, sequence differences determine the topology of the protein early along the folding pathway, which help to explain the process by which one fold can evolve into another. [ABSTRACT FROM AUTHOR]

The self-assembly of β2-microglobuhn into fibrils leads to dialysis-related amyloidosis. pH- mediated partial unfolding is required for the formation of the amyloidogenic intermediate that then self- assembles into amyloid fibrils. Two partially folded intermediates of β2-microglobulin have been identified experimentally and linked to the formation of fibrils of distinct morphology, yet it remains difficult to characterize these partially unfolded states at high resolution using experimental approaches. Consequently, we have performed molecular dynamics simulations at neutral and low pH to determine the structures of these partially unfolded amyloidogenic intermediates. In the low-pH simulations, we observed the formation of a-sheet structure, which was first proposed by Pauling and Corey. Multiple simulations were performed, and two distinct intermediate state ensembles were identified that may account for the different fibril morphologies. The predominant early unfolding intermediate was nativelike in structure, in agreement with previous NMR studies. The late unfolding intermediate was significantly disordered, but it maintained an extended elongated structure, with hydrophobic clusters and residual a-extended chain strands in specific regions of the sequence that map to amyloidogenic peptides. We propose that the formation of a-sheet facilitates self-assembly into partially unfolded prefibrillar amyloidogenic intermediates. [ABSTRACT FROM AUTHOR]

Performs direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2. Calculation of free energy perturbation using transition and denature-state structures; Conduction of molecular dynamic simulations for the thermal denaturation of enzyme inhibitor.

Analyzes the folding and unfolding pathway of barnase using a method similar to the classical Bronsted-beta approach. Description of the unfolding of wild-type barnase and the Y17G and 188V mutants; Characterization of the transition state of unfolding; Effect of mutations on the unfolding pathway; Effect of mutations on the transition state of unfolding.

Examines the molecular mechanism of stabilization of proteins by trimethylamine n-oxide (TMAO). Solubilities of a homologous series of cyclic dipeptides; Interaction between TMAO solution and the amide unit; Increase of the number of hydrogen bond.