Zhen Xia

RNA 3D Structure Prediction by Using a Coarse-Grained Model and Experimental Data

RNAs form complex secondary and three-dimensional structures, and their biological functions highly rely on their structures and dynamics. Here we developed a general coarse-grained framework for RNA 3D structure prediction. A new, hybrid coarse-grained model that explicitly describes the electrostatics and hydrogen-bond interactions has been constructed based on experimental structural statistics. With the simulated annealing simulation protocol, several RNAs of less than 30-nt were folded to within 4.0 Å of the native structures. In addition, with limited restraints on Watson-Crick basepairing based on the data from NMR spectroscopy and small-angle X-ray scattering (SAXS) information, the current model was able to characterize the complex tertiary structures of large size RNAs, such as 5S ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg(2+) cations and limited basepairing restraints were included. The accuracy of our model has been compared favorably with other RNA structure prediction methods presented in the previous study of RNA-Puzzles. Therefore the coarse-grained model presented here offers a unique approach for accurate prediction and modeling of RNA structures.

Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process

The recognition mechanism and cleavage activity of argonaute (Ago), miRNA, and mRNA complexes are the core processes to the small non-coding RNA world. The 5′ nucleation at the ‘seed’ region (position 2–8) of miRNA was believed to play a significant role in guiding the recognition of target mRNAs to the given miRNA family. In this paper, we have performed all-atom molecular dynamics simulations of the related and recently revealed Ago-DNA:mRNA ternary complexes to study the dynamics of the guide-target recognition and the effect of mutations by introducing “damaging” C·C mismatches at different positions in the seed region of the DNA-RNA duplex. Our simulations show that the A-form-like helix duplex gradually distorts as the number of seed mismatches increases and the complex can survive no more than two such mismatches. Severe distortions of the guide-target heteroduplex are observed in the ruinous 4-sites mismatch mutant, which give rise to a bending motion of the PAZ domain along the L1/L2 “hinge-like” connection segment, resulting in the opening of the nucleic-acid-binding channel. These long-range interactions between the seed region and PAZ domain, moderated by the L1/L2 segments, reveal the central role of the seed region in the guide-target strands recognition: it not only determines the guide-target heteroduplex’s nucleation and propagation, but also regulates the dynamic motions of Ago domains around the nucleic-acid-binding channel.

The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).

Progress in understanding protein folding relies heavily upon an interplay between experiment and theory. In particular, readily interpretable experimental data that can be meaningfully compared to simulations are required. According to standard mutational ϕ analysis, the transition state for Protein L contains only a single hairpin. However, we demonstrate here using ψ analysis with engineered metal ion binding sites that the transition state is extensive, containing the entire four-stranded β sheet. Underreporting of the structural content of the transition state by ϕ analysis also occurs for acyl phosphatase [Pandit, A. D., Jha, A., Freed, K. F. & Sosnick, T. R., (2006). Small proteins fold through transition states with native-like topologies. J. Mol. Biol.361, 755-770], ubiquitin [Sosnick, T. R., Dothager, R. S. & Krantz, B. A., (2004). Differences in the folding transition state of ubiquitin indicated by ϕ and ψ analyses. Proc. Natl Acad. Sci. USA 101, 17377-17382] and BdpA [Baxa, M., Freed, K. F. & Sosnick, T. R., (2008). Quantifying the structural requirements of the folding transition state of protein A and other systems. J. Mol. Biol.381, 1362-1381]. The carboxy-terminal hairpin in the transition state of Protein L is found to be nonnative, a significant result that agrees with our Protein Data Bank-based backbone sampling and all-atom simulations. The nonnative character partially explains the failure of accepted experimental and native-centric computational approaches to adequately describe the transition state. Hence, caution is required even when an apparent agreement exists between experiment and theory, thus highlighting the importance of having alternative methods for characterizing transition states.

UV-radiation Induced Disruption of Dry-Cavities in Human γD-crystallin Results in Decreased Stability and Faster Unfolding

Age-onset cataracts are believed to be expedited by the accumulation of UV-damaged human γD-crystallins in the eye lens. Here we show with molecular dynamics simulations that the stability of γD-crystallin is greatly reduced by the conversion of tryptophan to kynurenine due to UV-radiation, consistent with previous experimental evidences. Furthermore, our atomic-detailed results reveal that kynurenine attracts more waters and other polar sidechains due to its additional amino and carbonyl groups on the damaged tryptophan sidechain, thus breaching the integrity of nearby dry center regions formed by the two Greek key motifs in each domain. The damaged tryptophan residues cause large fluctuations in the Tyr-Trp-Tyr sandwich-like hydrophobic clusters, which in turn break crucial hydrogen-bonds bridging two β-strands in the Greek key motifs at the “tyrosine corner”. Our findings may provide new insights for understanding of the molecular mechanism of the initial stages of UV-induced cataractogenesis.

A Review of Physics-Based Coarse-Grained Potentials for the Simulations of Protein Structure and Dynamics

Abstract By simplifying the atomistic representation of a biomolecular system, coarse-grained (CG) approach enables the molecular dynamics simulation to reveal the biological processes, which occur on the time and length scales that are inaccessible to the all-atom models. Many CG physical models have been developed over the years. Here, we review the general CG force field models, which have been developed by following the fundamental physical principles. Such physics-based CG potentials have higher degree of transferability and broader applications when compared with the effective potentials, which are derived from specific molecular systems and environments. We expect growing interests in developing and applying general CG force fields at different levels of problems such as protein dynamics and structure prediction.

The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function.

Immune control of viral infections is modulated by diverse T cell receptor (TCR) clonotypes engaging peptide-MHC class I complexes on infected cells, but the relationship between TCR structure and antiviral function is unclear. Here we apply in silico molecular modeling with in vivo mutagenesis studies to investigate TCR-pMHC interactions from multiple CTL clonotypes specific for a well-defined HIV-1 epitope. Our molecular dynamics simulations of viral peptide-HLA-TCR complexes, based on two independent co-crystal structure templates, reveal that effective and ineffective clonotypes bind to the terminal portions of the peptide-MHC through similar salt bridges, but their hydrophobic side-chain packings can be very different, which accounts for the major part of the differences among these clonotypes. Non-specific hydrogen bonding to viral peptide also accommodates greater epitope variants. Furthermore, free energy perturbation calculations for point mutations on the viral peptide KK10 show excellent agreement with in vivo mutagenesis assays, with new predictions confirmed by additional experiments. These findings indicate a direct structural basis for heterogeneous CTL antiviral function.

Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar

Significance An outstanding issue in protein science is identifying the relationship between sequence and folding, e.g., do sequences having similar structures have similar folding pathways? The homologs Proteins G & L have been cited as a primary example where sequence variations dramatically affect folding dynamics. However, our new results indicate that the homologs have similar folding behavior. At the highest point on the reaction surface, the pathways converge to similar ensembles. These findings are distinct from descriptions based on the widely used mutational ϕ analysis, partly due to nonnative behavior. Our study emphasizes that significant challenges remain both in characterizing and predicting transition state ensembles even for relatively simple proteins whose folding behavior is believed to be well understood. Experimental and computational folding studies of Proteins L & G and NuG2 typically find that sequence differences determine which of the two hairpins is formed in the transition state ensemble (TSE). However, our recent work on Protein L finds that its TSE contains both hairpins, compelling a reassessment of the influence of sequence on the folding behavior of the other two homologs. We characterize the TSEs for Protein G and NuG2b, a triple mutant of NuG2, using ψ analysis, a method for identifying contacts in the TSE. All three homologs are found to share a common and near-native TSE topology with interactions between all four strands. However, the helical content varies in the TSE, being largely absent in Proteins G & L but partially present in NuG2b. The variability likely arises from competing propensities for the formation of nonnative β turns in the naturally occurring proteins, as observed in our TerItFix folding algorithm. All-atom folding simulations of NuG2b recapitulate the observed TSEs with four strands for 5 of 27 transition paths [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. Our data support the view that homologous proteins have similar folding mechanisms, even when nonnative interactions are present in the transition state. These findings emphasize the ongoing challenge of accurately characterizing and predicting TSEs, even for relatively simple proteins.

Prediction and Coarse-Grained Modeling of RNA Structures

The discovery of a large number of RNAs of complex three-dimensional (3D) structures, associated with numerous functions in the cell, has led to a major paradigm shift in biology. Computer simulation of the higher-order structure and dynamics of an RNA can provide great insights into the properties of the RNA and its functions in the cell. In recent years, steady progress has been made toward the RNA 3D structure prediction and modeling with an increasing number of advanced algorithms and models. Here, we describe recent advances in RNA structure prediction using coarse-grained approaches. We focus on the prediction strategies of different coarse-grained models according to their underlying physical or chemical principles. The strengths and the limitations of each model are discussed. We conclude by summarizing potential applications and the future directions of coarse-grained models for RNA structure prediction.

Multiscale modeling of RNA 3D structures

Balancing accuracy and computational efficiency while studying biomolecular structures and dynamics necessitates scalable modeling techniques. We have been developing a coarse-grained model for RNA that uses pseudoatoms in place of all-atom representation. By reducing the number of interactions and mean-field representation of environmental effects, significant improvement in computational efficiency is achieved in a comparison to all-atom based physical modeling approaches. A five bead coarse-grained model utilized for RNA 3D structure prediction is presented. Unique features of this framework include the direct mapping between all atom and coarse-grained models, incorporation of electrostatic interactions, continuous and analytical energy function that can be used in molecular dynamics simulations, and statistical derived parameters. Here we present the basic framework of our model and recent applications to RNA folding.