Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model

Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations

The phenazine biosynthetic pathway is of considerable importance for the pharmaceutical industry. The pathway produces two products: phenazine-1,6-dicarboxylic acid and phenazine-1-carboxylic acid. PhzF is an isomerase that catalyzes trans-2,3-dihydro-3-hydroxyanthranilic acid isomerization and plays an essential role in the phenazine biosynthetic pathway. Although the PhzF crystal structure has been determined recently, an understanding of the detailed catalytic mechanism and the roles of key catalytic residues are still lacking. In this study, a computational strategy using a combination of molecular modeling, molecular dynamics simulations, and quantum mechanics/molecular mechanics simulations was used to elucidate these important issues. The Apo enzyme, enzyme-substrate complexes with negatively charged Glu45, enzyme-transition state analog inhibitor complexes with neutral Glu45, and enzyme-product complexes with negatively charged Glu45 structures were optimized and modeled using a 200 ns molecular dynamics simulation. Residues such as Gly73, His74, Asp208, Gly212, Ser213, and water, which play important roles in ligand binding and the isomerization reaction, were comprehensively investigated. Our results suggest that the Glu45 residue at the active site of PhzF acts as a general base/acid catalyst during proton transfer. This study provides new insights into the detailed catalytic mechanism of PhzF and the results have important implications for PhzF modification.

The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations

1 Abstract

Turbulent phenomena in protein folding

Protein folding and hydrodynamic turbulence are two long-standing challenges, in molecular biophysics and fluid dynamics, respectively. The theories of these phenomena have been developed independently and used different formalisms. Here we show that the protein folding flows can be surprisingly similar to turbulent fluid flows. Studying a benchmark model protein (an SH3 domain), we have found that the flows for the slow folding trajectories of the protein, in which a partly formed N- and C-terminal β sheet hinders the RT loop from attaching to the protein core, have many properties of turbulent flows of a fluid. The flows are analyzed in a three-dimensional (3D) space of collective variables, which are the numbers of native contacts between the terminal β strands, between the RT loop and the protein core, and the rest of the native contacts. We have found that the flows have fractal nature and are filled with 3D eddies; the latter contain strange attractors, at which the tracer flow paths behave as saddle trajectories. Two regions of the space increment have been observed, in which the flux variations are self-similar with the scaling exponent h=1/3, in surprising agreement with the Kolmogorov inertial range theory of turbulence. In one region, the cascade of protein rearrangements is directed from larger to smaller scales (net folding), and in the other, it is oppositely directed (net unfolding). Folding flows for the fast trajectories are essentially "laminar" and do not have the property of self-similarity. Based on the results of our study, we infer, and support this inference by simulations, that the origin of the similarity between the protein folding and turbulent motion of a fluid is in a cascade mechanism of structural transformations in the systems that underlies these phenomena.

Universal partitioning of the hierarchical fold network of 50-residue segments in proteins

Background

Several studies have demonstrated that protein fold space is structured hierarchically and that power-law statistics are satisfied in relation between the numbers of protein families and protein folds (or superfamilies). We examined the internal structure and statistics in the fold space of 50 amino-acid residue segments taken from various protein folds. We used inter-residue contact patterns to measure the tertiary structural similarity among segments. Using this similarity measure, the segments were classified into a number (K_c) of clusters. We examined various K_c values for the clustering. The special resolution to differentiate the segment tertiary structures increases with increasing K_c. Furthermore, we constructed networks by linking structurally similar clusters.

Results

The network was partitioned persistently into four regions for K_c ≥ 1000. This main partitioning is consistent with results of earlier studies, where similar partitioning was reported in classifying protein domain structures. Furthermore, the network was partitioned naturally into several dozens of sub-networks (i.e., communities). Therefore, intra-sub-network clusters were mutually connected with numerous links, although inter-sub-network ones were rarely done with few links. For K_c ≥ 1000, the major sub-networks were about 40; the contents of the major sub-networks were conserved. This sub-partitioning is a novel finding, suggesting that the network is structured hierarchically: Segments construct a cluster, clusters form a sub-network, and sub-networks constitute a region. Additionally, the network was characterized by non-power-law statistics, which is also a novel finding.

Conclusion

Main findings are: (1) The universe of 50 residue segments found here was characterized by non-power-law statistics. Therefore, the universe differs from those ever reported for the protein domains. (2) The 50-residue segments were partitioned persistently and universally into some dozens (ca. 40) of major sub-networks, irrespective of the number of clusters. (3) These major sub-networks encompassed 90% of all segments. Consequently, the protein tertiary structure is constructed using the dozens of elements (sub-networks).

Folding of the 25 Residue Aβ(12−36) Peptide in TFE/Water: Temperature-Dependent Transition from a Funneled Free-Energy Landscape to a Rugged One

The free-energy landscape of the Alzheimer beta-amyloid peptide Abeta(12-36) in a 40% (v/v) 2,2,2-trifluoroethanol (TFE)/water solution was determined by using multicanonical molecular dynamics simulations. Simulations using this enhanced conformational sampling technique were initiated from a random unfolded polypeptide conformation. Our simulations reliably folded the peptide to the experimental NMR structure, which consists of two linked helices. The shape of the free energy landscape for folding was found to be strongly dependent on temperature: Above 325 K, the overall shape was funnel-like, with the bottom of the funnel coinciding exactly with the NMR structure. Below 325 K, on the other hand, the landscape became increasingly rugged, with the emergence of new conformational clusters connected by low free-energy pathways. Finally, our simulations reveal that water and TFE solvate the polypeptide in different ways: The hydrogen bond formation between TFE and Abeta was enhanced with decreasing temperature, while that between water and Abeta was depressed.