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REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.

ABSTRACT: Protein structure prediction approaches usually perform modeling simulations based on reduced representation of protein structures. For biological utilizations, it is an important step to construct full atomic models from the reduced structure decoys. Most of the current full atomic model reconstruction procedures have defects which either could not completely remove the steric clashes among backbone atoms or generate final atomic models with worse topology similarity relative to the native structures than the reduced models. In this work, we develop a new protocol, called REMO, to generate full atomic protein models by optimizing the hydrogen-bonding network with basic fragments matched from a newly constructed backbone isomer library of solved protein structures. The algorithm is benchmarked on 230 nonhomologous proteins with reduced structure decoys generated by I-TASSER simulations. The results show that REMO has a significant ability to remove steric clashes, and meanwhile retains good topology of the reduced model. The hydrogen-bonding network of the final models is dramatically improved during the procedure. The REMO algorithm has been exploited in the recent CASP8 experiment which demonstrated significant improvements of the I-TASSER models in both atomic-level structural refinement and hydrogen-bonding network construction.

SUBMITTER: Li Y

PROVIDER: S-EPMC2771173 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature

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REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.

Li Yunqi Y Zhang Yang Y

Proteins 20090801 3

Protein structure prediction approaches usually perform modeling simulations based on reduced representation of protein structures. For biological utilizations, it is an important step to construct full atomic models from the reduced structure decoys. Most of the current full atomic model reconstruction procedures have defects which either could not completely remove the steric clashes among backbone atoms or generate final atomic models with worse topology similarity relative to the native stru ...[more]

PMID: 19274737

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Project description:The determination of the full crystal structure of the uranyl sulfate mineral uranopilite, (UO2)6(SO4)O2(OH)6·14H2O, including the positions of the hydrogen atoms within the corresponding unit cell, has not been feasible to date due to the poor quality of its X-ray diffraction pattern. In this paper, the complete crystal structure of uranopilite is established for the first time by means of first principles solid-state calculations based in density functional theory employing a large plane wave basis set and pseudopotential functions. The computed unit-cell parameters and structural data for the non-hydrogen atoms are in excellent agreement with the available experimental data. The computed X-ray diffraction pattern is also in satisfactory agreement with the experimental pattern. The infrared spectrum of uranopilite is collected from a natural crystal specimen originating in Jáchymov (Czech Republic) and computed employing density functional perturbation theory. The theoretical and experimental vibrational spectra are highly consistent. Therefore, a full assignment of the bands in the experimental infrared spectrum is performed using a normal mode analysis of the first principles vibrational results. One overtone and six combination bands are recognized in the infrared spectrum. The elasticity tensor and phonon spectra of uranopilite are computed from the optimized crystal structure and used to analyze its mechanical stability, to obtain a rich set of elastic properties and to derive its fundamental thermodynamic properties as a function of temperature. Uranopilite is shown to have a large mechanical anisotropy and to exhibit the negative Poisson's ratio and negative linear compressibility phenomena. The calculated specific heat and entropy at 298.15 K are 179.6 and 209.0 J K-1 mol-1, respectively. The computed fundamental thermodynamic functions of uranopilite are employed to obtain its thermodynamic functions of formation in terms of the elements and the thermodynamic properties of a set of chemical reactions relating uranopilite with a representative group of secondary phases of spent nuclear fuel. From the reaction thermodynamic data, the relative stability of uranopilite with respect to these secondary phases is evaluated as a function of temperature and under different hydrogen peroxide concentrations. From the results, it follows that uranopilite has a very large thermodynamic stability in the presence of hydrogen peroxide. The high stability of uranopilite under this condition justify its early crystallization in the paragenetic sequence of secondary phases occurring when uranium dioxide is exposed to sulfur-rich solutions.

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REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.

Publications

REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.

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