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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

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.

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.

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.

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.

The need for data-centric scientific tools is growing; domains such as biology, chemistry, and physics are increasingly adopting computational approaches. So, scientists must deal with the challenges of big data. To address these challenges, researchers built a visual-analytics platform named DIVE (Data Intensive Visualization Engine). DIVE is a data-agnostic, ontologically expressive software framework that can stream large datasets at interactive speeds. In particular, DIVE makes novel contributions to structured-data-model manipulation and high-throughput streaming of large, structured datasets. [ABSTRACT FROM AUTHOR]

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.