Macromolecular Structural Research Articles

Computational modeling of protein–RNA complex structures

Protein–RNA interactions play fundamental roles in many biological processes, such as regulation of gene expression, RNA splicing, and protein synthesis. The understanding of these processes improves as new structures of protein–RNA complexes are solved and the molecular details of interactions analyzed. However, experimental determination of protein–RNA complex structures by high-resolution methods is tedious and difficult. Therefore, studies on protein–RNA recognition and complex formation present major technical challenges for macromolecular structural biology. Alternatively, protein–RNA interactions can be predicted by computational methods. Although less accurate than experimental measurements, theoretical models of macromolecular structures can be sufficiently accurate to prompt functional hypotheses and guide e.g. identification of important amino acid or nucleotide residues. In this article we present an overview of strategies and methods for computational modeling of protein–RNA complexes, including software developed in our laboratory, and illustrate it with practical examples of structural predictions.

Construction of macromolecular structural model of anthracite from Chengzhuang coal mine and its molecular simulation

The macromolecular structure model of Chengzhuang coal was constructed based on the results of proximate and ultimate analysis, 13C-NMR spectrum and XPS spectrum. In the model the numbers of rings in polycyclic aromatic hydrocarbon were distributed between 1 and 5. The aliphatic C atoms existed in the forms of -CH3, -CH2- and cycloalkanes. 9 atoms of O were in the form of C=O, while one in the form of -OH and another one in the form of -O-. 2 atoms of N were in pyrrole, while S atom did not appear in the model because its concentration was lower than 1%. Molecular mechanics (MM) and molecular dynamics (MD) was adopted to simulate the energy-minimum conformation of the model and the results showed that the aromatic layers tended to be parallel by intramolecular or intermolecular π-π interaction and the latter should be one of the main contributors for the short-range ordering of high-rank coal structure. The van der Waals energy and hydrogen bond energy contributed to the energy-minimum conformation.

Novel insights through the integration of structural and functional genomics data with protein networks

In recent years, major advances in genomics, proteomics, macromolecular structure determination, and the computational resources capable of processing and disseminating the large volumes of data generated by each have played major roles in advancing a more systems-oriented appreciation of biological organization. One product of systems biology has been the delineation of graph models for describing genome-wide protein-protein interaction networks. The network organization and topology which emerges in such models may be used to address fundamental questions in an array of cellular processes, as well as biological features intrinsic to the constituent proteins (or "nodes") themselves. However, graph models alone constitute an abstraction which neglects the underlying biological and physical reality that the network's nodes and edges are highly heterogeneous entities. Here, we explore some of the advantages of introducing a protein structural dimension to such models, as the marriage of conventional network representations with macromolecular structural data helps to place static node and edge constructs in a biologically more meaningful context. We emphasize that 3D protein structures constitute a valuable conceptual and predictive framework by discussing examples of the insights provided, such as enabling in silico predictions of protein-protein interactions, providing rational and compelling classification schemes for network elements, as well as revealing interesting intrinsic differences between distinct node types, such as disorder and evolutionary features, which may then be rationalized in light of their respective functions within networks.

Model construction of the macromolecular structure of Yanzhou Coal and its molecular simulation

Based on proximate and ultimate analysis, 13C CP/MAS NMR data of Yanzhou coal, a macromolecular structural model was constructed. In this model, benzene is the main aromatic compound and aliphatic structure exists mainly in the forms of aliphatic side chains, cycloalkanes and hydrogenated aromatic rings. The methyl proportion is similar to the total proportion of methylene and methine groups. Seventeen O atoms are present as carboxyl, carbonyl and hydroxyl groups and three N atoms exist in the forms of pyridine and pyrrole, while five S atoms in the form of thiophenic S. Molecular mechanics (MM) and molecular dynamics (MD) techniques were used to carry out energy minimization simulations on this model. The simulation results indicate that stabilization of the macromolecular structure is due to the energies of van der Waals, torsion, angle, bond and inversion in descending order of importance, and intramolecular π–π interactions between aromatic layers enables their quasi-parallel arrangement. Semi-empirical quantum chemistry (AM1) simulation indicates that the C–C bonds adjacent to carbonyl C atoms exhibit higher activity, and C atoms adjacent to S atoms and terminal C atoms are more negatively charged, which therefore prone to undergo oxidation reactions, while aromatic C atoms are characterized by fewer charges and very high stability.

Macromolecular structure of the organic framework of nacre in Haliotis rufescens: Implications for growth and mechanical behavior

We have performed a macromolecular structural analysis of the interlamellar and intertabular parts of the organic framework of the nacreous part of the shell of Haliotis rufescens, including the identification of structural chitin. Using histochemical optical microscopy we have mapped the locations of carboxylates and sulfates of proteins and chitin on the surfaces and within the core of the interlamellar layers and the intertabular matrix that together form the external organic matrix of composite nacre. This extends the earlier work of Nudelmann et al. [Nudelman, F., Gotliv, B.A., Addadi, L. and Weiner, S. 2006. Mollusk shell formation: mapping the distribution of organic matrix components underlying a single aragonite tablet in nacre. J. Struct. Biol. 153, 176-187] and Crenshaw and Ristedt [Crenshaw, M.A., Ristedt, H. 1976. The histochemical localization of reactive groups in septal nacre from Nautilus pompilius. In: Omori, M., Watabe, N. (Eds.) The Mechanisms of Biomineralization in Animals and Plants. Tokai University Press, Toyko] on Nautilus pompilius. Our mapping identifies distinct regions, defined by the macromolecular groups, including what is proposed to be the sites of CaCO(3) nucleation and that play a key role in nacre growth. Using AFM scanning probe microscopy we have identified a fibrous core within the framework that we associate with chitin. The structural picture that is evolved is then used to develop a simple structural model for the organic framework which is shown to be consistent with mechanical property measurements. The role of the intracrystalline matrix within the nacre tablets in mediating nacre's mechanical response is noted within the framework of our model.

Mapping Functionally Important Motifs SPF and GGQ of the Decoding Release Factor RF2 to the Escherichia coli Ribosome by Hydroxyl Radical Footprinting: IMPLICATIONS FOR MACROMOLECULAR MIMICRY AND STRUCTURAL CHANGES IN RF2

The function of the decoding release factor (RF) in translation termination is to couple cognate recognition of the stop codon in the mRNA with hydrolysis of the completed polypeptide from its covalently linked tRNA. For this to occur, the RF must interact with specific A-site components of the active centers within both the small and large ribosomal subunits. In this work, we have used directed hydroxyl radical footprinting to map the ribosomal binding site of the Escherichia coli class I release factor RF2, during translation termination. In the presence of the cognate UGA stop codon, residues flanking the universally conserved (250)GGQ(252) motif of RF2 were each shown to footprint to the large ribosomal subunit, specifically to conserved elements of the peptidyltransferase and GTPase-associated centers. In contrast, residues that flank the putative "peptide anticodon" of RF2, (205)SPF(207), were shown to make a footprint in the small ribosomal subunit at positions within well characterized 16 S rRNA motifs in the vicinity of the decoding center. Within the recently solved crystal structure of E. coli RF2, the GGQ and SPF motifs are separated by 23 A only, a distance that is incompatible with the observed cleavage sites that are up to 100 A apart. Our data suggest that RF2 may undergo gross conformational changes upon ribosome binding, the implications of which are discussed in terms of the mechanism of RF-mediated termination.

Imaging of humic substance macromolecular structures in water and soils

Humic substances (HSs) are the natural organic polyelectrolytes formed from the biochemical weathering of plant and animal remains. Their macromolecular structure and chemistry determine their role in biogeochemical processes. In situ spectromicroscopic evidence showed that the HS macromolecular structures (size and shape) vary as a function of HS origin (soil versus fluvial), solution chemistry, and the associated mineralogy. The HSs do not simply form coils in acidic or strong electrolyte solutions and elongated structures in dilute alkaline solutions. The macromolecular structural changes of HSs are likely to modify contaminant solubility, biotransformation, and the carbon cycle in soils and sediments.

Macromolecular structural elucidation with solid-state NMR-derived orientational constraints

The complete structure determination of a polypeptide in a lipid bilayer environment is demonstrated built solely upon orientational constraints derived from solid-state NMR observations. Such constraints are obtained from isotopically labeled samples uniformly aligned with respect to the B(0) field. Each observation constrains the molecular frame with respect to B(0) and the bilayer normal, which are arranged to be parallel. These constraints are not only very precise ( a few tenths of a degree), but also very accurate. This is clearly demonstrated as the backbone structure is assembled sequentially and the i to i + 6 hydrogen bonds in this structure of the gramicidin channel are shown on average to be within 0.5 A of ideal geometry. Similarly, the side chains are assembled independently and in a radial direction from the backbone. The lack of considerable atomic overlap between side chains also demonstrates the accuracy of the constraints. Through this complete structure, solid-state NMR is demonstrated as an approach for determining three-dimensional macromolecular structure.