Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data

The Dynameomics project is our effort to characterize the native-state dynamics and folding/unfolding pathways of representatives of all known protein folds by way of molecular dynamics simulations, as described by Beck et al. (in Protein Eng. Des. Select., the first paper in this series). The data produced by these simulations are highly multidimensional in structure and multi-terabytes in size. Both of these features present significant challenges for storage, retrieval and analysis. For optimal data modeling and flexibility, we needed a platform that supported both multidimensional indices and hierarchical relationships between related types of data and that could be integrated within our data warehouse, as described in the accompanying paper directly preceding this one. For these reasons, we have chosen On-line Analytical Processing (OLAP), a multi-dimensional analysis optimized database, as an analytical platform for these data. OLAP is a mature technology in the financial sector, but it has not been used extensively for scientific analysis. Our project is further more unusual for its focus on the multidimensional and analytical capabilities of OLAP rather than its aggregation capacities. The dimensional data model and hierarchies are very flexible. The query language is concise for complex analysis and rapid data retrieval. OLAP shows great promise for the dynamic protein analysis for bioengineering and biomedical applications. In addition, OLAP may have similar potential for other scientific and engineering applications involving large and complex datasets.     

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

The goal of Dynameomics is to perform atomistic molecular dynamics (MD) simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways. Here we present 188-fold representatives and their native state simulations and analyses. These 188 targets represent 67% of all the structures in the Protein Data Bank. The behavior of several specific targets is highlighted to illustrate general properties in the full dataset and to demonstrate the role of MD in understanding protein function and stability. As an example of what can be learned from mining the Dynameomics database, we identified a protein fold with heightened localized dynamics. In one member of this fold family, the motion affects the exposure of its phosphorylation site and acts as an entropy sink to offset another portion of the protein that is relatively immobile in order to present a consistent interface for protein docking. In another member of this family, a polymorphism in the highly mobile region leads to a host of disease phenotypes. We have constructed a web site to provide access to a novel hybrid relational/multidimensional database (described in the succeeding two papers) to view and interrogate simulations of the top 30 targets: http://www.dynameomics.org. The Dynameomics database, currently the largest collection of protein simulations and protein structures in the world, should also be useful for determining the rules governing protein folding and kinetic stability, which should aid in deciphering genomic information and for protein engineering and design.     

GRAFTER: a computational aid for the design of novel proteins

The GRAFTER suite of programs provides geometric search andevaluation functions that simplify and automate the processof identifying the best scaffolds for a particular structuralmotif. Three applications of the GRAFTER suite are presented.Potential grafts between repressor and 434 repressor were identifiedthat should change the DNA binding specificity of these repressors.These results are compared with site-directed mutagenesis experimentsthat have been shown to alter repressor-DNA binding specificity.Next, 26 loops from antibody structures were grouped into familiesof similar structure. Grafts of antibody loops onto a pre-existingscaffold are an essential component of antibody humanization.Finally, interleukin (lL)-4 was searched as a scaffold thatmight accept the graft of a five residue epitope from humangrowth hormone (hGH). The existence of a crystal structure ofthe hGH-hGH receptor complex, extensive mutagenesis studiesof the hGH residues that contribute to the energetics of ligand-receptorinteractions and the gross structural homology between hGH andIL-4 make this an appealing computational target. The approachpresented here could aid the development of novel enzymes andbinding proteins     

A method for computational combinatorial peptide design of inhibitors of Ras protein

A computational combinatorial approach is proposed for the designof a peptide inhibitor of Ras protein. The procedure involvesthree steps. First, a `Multiple Copy Simultaneous Search' identifiesthe location of specific functional groups on the Ras surface.This search method allowed us to identify an important bindingsurface consisting of two ß strands (residues 5–8and 52–56), in addition to the well known Ras effectorloop and switch II region. The two ß strands had not previouslybeen reported to be involved in Ras–Raf interaction. Second,after constructing the peptide inhibitor chain based on thelocation of N-methylacetamide (NMA) minima, functional groupsare selected and connected to the main chain C atom. This stepgenerates a number of possible peptides with different sequenceson the Ras surface. Third, potential inhibitors are designedbased on a sequence alignment of the peptides generated in thesecond step. This computational approach reproduces the conservedpattern of hydrophobic, hydrophilic and charged amino acidsidentified from the Ras effectors. The advantages and limitationsof this approach are discussed.     

Intermediates in the protein folding process: a computational model

The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage-ES and the late stage-LS) is verified using two proteins, one of which is treated (according to experimental observations) as the early stage and the second as an example of the LS step. The early stage is based solely on backbone structural preferences, while the LS model takes into account the water environment, treated as an external hydrophobic force field and represented by a 3D Gauss function. The characteristics of 1ZTR (the ES intermediate, as compared with 1ENH, which is the LS intermediate) confirm the link between the gradual disappearance of ES characteristics in LS structural forms and the simultaneous emergence of LS properties in the 1ENH protein. Positive verification of ES and LS characteristics in these two proteins (1ZTR and 1ENH respectively) suggest potential applicability of the presented model to in silico protein folding simulations.     

Molecular dynamics simulations as a tool for improving protein stability

Haloalkane dehalogenase (DhlA) was used as a model protein toexplore the possibility to use molecular dynamics (MD) simulationsas a tool to identify flexible regions in proteins that canserve as a target for stability enhancement by introductionof a disulfide bond. DhlA consists of two domains: an     

Experimental and computational mapping of the binding surface of a crystalline protein

Multiple Solvent Crystal Structures (MSCS) is a crystallographictechnique to identify energetically favorable positions andorientations of small organic molecules on the surface of proteins.We determined the high-resolution crystal structures of thermolysin(TLN), generated from crystals soaked in 50–70% acetone,50–80% acetonitrile and 50 mM phenol. The structures ofthe protein in the aqueous–organic mixtures are essentiallythe same as the native enzyme and a number of solvent interactionsites were identified. The distribution of probe molecules showsclusters in the main specificity pocket of the active site anda buried subsite. Within the active site, we compared the experimentallydetermined solvent positions with predictions from two computationalfunctional group mapping techniques, GRID and Multiple CopySimultaneous Search (MCSS). The experimentally determined smallmolecule positions are consistent with the structures of knownprotein–ligand complexes of TLN.     

Analysis of isothermal annular jets: Comparison of computational fluid dynamics and experimental data

A computational fluid dynamics technique was developed for the simulation of airflow through an annular jet. The technique used a commercial simulation package with a Reynolds stress model for the simulation of turbulent flows. The model parameters were calibrated using available experimental data for circular and annular jets. It was found that, after this calibration, the computational results agreed well with experimental data (specifically, with the velocity magnitude, velocity decay rate, and the velocity spreading rate). The jet geometry studied was based on industrial melt‐blowing nozzles. The velocities studied varied from the low subsonic incompressible range to nearly sonic conditions. Based on both the computational and experimental results, a correlation was proposed that predicts the centerline velocity profiles in both the near‐ and far‐field regions. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 94: 909–922, 2004     

Potential of genetic algorithms in protein folding and protein engineering simulations

Genetic algorithms are very efficient search mechanisms whichmutate, recombine and select amongst tentative solutions toa problem until a near optimal one is achieved. We introducethem as a new tool to study proteins. The identification andmotivation for different fitness functions is discussed. Theevolution of the zinc finger sequence motif from a random startis modelled. User specified changes of the repressor structurewere simulated and critical sites and exchanges for mutagenesisidentified. Vast conformational spaces are efficiently searchedas illustrated by the ab initio folding of a model protein ofa four ß strand bundle. The genetic algorithm simulationwhich mimicked important folding constraints as overall hydrophobicpackaging and a propensity of the betaphilic residues for transpositions achieved a unique fold. Cooperativity in the ßstrand regions and a length of 3–5 for the interconnectingloops was critical. Specific interaction sites were considerablyless effective in driving the fold.     

磨削加工科学数据共享平台的开发

平台开发以郑州市科学数据共享平台为实现与应用技术指标,利用MySQL5.0作为后台数据库,Tomcat5.5作为Web服务器,采用J2EE体系结构、MVC构架,实现对数据库平台的创建、发布和管理功能。数据信息通过对磨削加工及其相关专业领域的搜集、组织与技术加工,构建了磨削工具库、设备库、学术论文库、行业动态库、技术标准库、专业著作书目库、厂商库、网址库及科技文献题录库等9个数据库,收录文献类型包括:学术论文、会议文献、汇编、工具图片及规格、设备图片及规格、国家和行业技术标准、网络数字资源等各类科技文献信息。     

A computational fluid dynamics design of a carbon dioxide sorption circulating fluidized bed

A kinetic theory based hydrodynamic model with experimentally determined sorption rates for reaction of CO₂ with K₂CO₃ solid sorbent is used to design a compact circulating fluidized bed sorption‐regeneration system for CO₂ removal from flue gases. Because of high solids fluxes, the sorber does not require internal or external cooling. The output is verified by computing the granular temperatures, particle viscosities, dispersion, and mass transfer coefficients. These properties agree with reported measurement values except the radial dispersion coefficients, which are much higher due to the larger bed diameter. With the solid sorbent prepared according to published information, the CO₂ removal percentage at the riser top is 69.16%. To improve the CO₂ removal, an effort is needed to develop a better sorbent or to simply lower the inlet gas velocity to operate in a denser mode, leading to a larger system. Also, the effect of temperature rise on the removal efficiency is investigated. © 2010 American Institute of Chemical Engineers AIChE J, 2010     

Comparison of experimental and computational functional group mapping of an RNase A structure: implications for computer-aided drug design

One relatively new computational approach to the drug discoveryprocess involves calculating functional group maps of a targetstructure. Experimental functional group mapping techniqueshave also recently emerged. In this paper, the structure ofRNase A with two bound formates (i.e. carboxylate functionalities)is used as a model system to test the computational methodology.Functional group maps of the RNase A structure were calculatedusing the Multiple Copy Simultaneous Search (MCSS) method andcompared with experimentally determined formate and water positions.The calculations indicate that the protonation state of active-sitehistidines determines the ability of the enzyme to bind formate.The results also suggest an ordered binding mechanism for thetwo formates. An improved strategy for using the MCSS methodto design new candidate ligands is discussed.     

Cholesterol oxidases: a study of nature's approach to protein design

Cholesterol oxidases are important as clinical reagents, potential larvicides, and tools in cell biology, and they are implicated in bacterial pathogenesis. Here we review chemical aspects of their function. We describe our current structural and mechanistic understanding of the type I and II cholesterol oxidases, our identification of an NH-pi hydrogen bond motif for stabilization of reduced flavins, our structural hypothesis of how O(2) gains access to the flavin, and our present understanding of type I cholesterol oxidase-lipid bilayer interactions.     

Crystal structure of a synthetic cyclodecapeptide for template-assembled synthetic protein design

The structural prototype of a new generation of regioselectively addressable functionalized templates (RAFTs) for use in protein de novo design has been synthesized and crystallized. The structure of the aromatically substituted cyclodecapeptide was determined by X-ray diffraction; it consists of an antiparallel beta sheet spanned by heterochirally induced type IIprime prime or minute beta turns, similar to that observed in gramicidin S. The three-dimensional structure of the artificial template was also examined by an NMR spectroscopic analysis in solution and shown to be compatible with a beta-sheet plane suitable for accommodating secondary functional peptide fragments for the synthesis of template-assembled synthetic proteins (TASPs).     

A systematic approach for the design of UV reactors using computational fluid dynamics

A wide variation exists in the geometries of UV reactors, which results in completely different hydrodynamics and therefore large differences with respect to the disinfection and oxidation performance. Among the large number of reactor types, it is not known beforehand which reactor type has the best performance with respect to disinfection or oxidation, and if such a reactor is the best reactor out of all the possible reactor designs. In this research, a systematic approach for the design of UV reactors is followed that makes use of computational fluid dynamics (CFD) modeling. To that end, the inactivation of Bacillus subtilis and degradation of atrazine was determined for a wide range of UV systems by means of CFD. The efficacy of UV systems was evaluated and improvements were made by taking measures that increase the mean dose and/or narrow the dose distribution, such as placing mirrors, enhancing the mixing and placing reactors in series. © 2010 American Institute of Chemical Engineers AIChE J, 2011     

Rational design of shape selective separation and catalysis—II: Mathematical model and computational studies

In our previous work [Gounaris, C.E., Floudas, C.A., Wei, J., 2006. Rational design of shape selective catalysis and separation: I. Concepts and analysis. Chemical Engineering Science, in press, doi: 10.1016/j.ces.2006.09.012], we introduced the concept of molecule projections, referred to as footprints, and briefly described rigorous criteria that define them. We also introduced the concept of strain index and showed how it can be used to identify portals that have the potential of being highly selective between two molecules. In this paper, we present in detail the mathematical formulations for the calculation of footprints and the complete mathematical model and algorithmic framework developed for the calculation of the strain index of any given molecule/portal pair. Thirty-eight molecules of interest, as well as a collection of 123 zeolite structures, involving 217 different windows, have been considered and selectivity results at ambient temperature are presented. A number of commercially interesting examples are studied in further detail, across a wide range of temperatures. It should be noted that the methodology is generic and can be applied for any pair of molecule and portal. The results indicate that there is a great potential in systems involving non-regular portals that are usually not considered in the selection process of a catalyst or molecular sieve.