Structure analysis of CCR5 from human and primates

It is well known that the chemokine receptor CCR5 plays very important roles in HIV-1 virus infection. A three-dimensional molecular model of human CCR5 was generated by SYBYL, a distance geometry-based homologous modeling package, using the corresponding transmembrane domain of bacteriorhodopsin as the template. On the basis of human CCR5 model, we also built 18 3D molecular models of CCR5 in primates from Pongo pygmaeus, Pygathrix nemaeus, Macaca assameniss, Trachy-pithecus phayrei, T. francoisi, M. arotoides, Rhinopithecus roxellance, R, bieti, R. avunculus, Hylobates leucogenys, Pan troglodytes, Gorilla gorilla, Cercopithecus aethiops 1, C. aethiops 2, Papio hamadryas M. mulatta, M. fascicularis and M. nemestrina. Structural analyses and statistics results suggested that the main-chains of the primate CCR5 were similar to that of the human CCR5 and that the fit-RMS deviation values of these primate CCR5 were less than 0.1 Angstrom. Moreover, the structures of these CCR5 proteins, except those of the African green monkey 1 (C.aet1), do not have a remarkable difference. It is proved that the 14th residue is possibly very important in the inhibition infections by M-tropic HIV-1, and it is also demonstrated that the 13th residue of human CCR5 was changed from asparagine into aspartic acid in all these primates. It means that the primate CCR5 no longer depend on CD4 for efficient entry, but human CCR5 may have evolved subsequently due to the use of CD4 as a receptor, allowing the high-affinity chemokine receptor-binding site of HIV to be sequestered from host immune surveillance. (C) 2000 Elsevier Science B.V. All rights reserved.

Inhibitors of Trypanosoma brucei trypanothione reductase: comparative molecular field analysis modeling and structural basis for selective inhibition

Background: Sleeping sickness is a major cause of death in Africa. Since no secure treatment is available, the development of novel therapeutic agents is urgent. In this context, the enzyme trypanothione reductase (TR) is a prominent molecular target that has been investigated in drug design for sleeping sickness. Results: In this study, comparative molecular field analysis models were generated for a series of Trypanosoma brucei TR inhibitors. Statistically significant results were obtained and the models were applied to predict the activity of external test sets, with good correlation between predicted and experimental results. We have also investigated the structural requirements for the selective inhibition of the parasite's enzyme over the human glutathione reductase. Conclusion: The quantitative structure-activity relationship models provided valuable information regarding the essential molecular requirements for the inhibitory activity upon the target protein, providing important insights into the design of more potent and selective TR inhibitors.

Mechanical analysis and modeling of structural archetypes

This is a research B for the University of Bologna. The course is the civil engineering LAUREA MAGISTRALE at UNIBO. The main purpose of this research is to promote another way of explaining, analyzing and presenting some civil engineering aspects to the students worldwide by theory, modeling and photos. The basic idea is divided into three steps. The first one is to present and analyze the theoretical parts. So a detailed analysis of the theory combined with theorems, explanations, examples and exercises will cover this step. At the second, a model will make clear all these parts that were discussed in the theory by showing how the structures work or fail. The modeling is able to present the behavior of many elements, in scale which we use in the real structures. After these two steps an interesting exhibition of photos from the real world with comments will give the chance to the engineers to observe all these theoretical and modeling-laboratory staff in many different cases. For example many civil engineers in the world may know about the air pressure on the structures but many of them have never seen the extraordinary behavior of the bridge of Tacoma ‘dancing with the air’. At this point I would like to say that what I have done is not a book, but a research of how this ‘3 step’ presentation or explanation of some mechanical characteristics could be helpful. I know that my research is something different and new and in my opinion is very important because it helps students to go deeper in the science and also gives new ideas and inspirations. This way of teaching can be used at all lessons especially at the technical. Hope that one day all the books will adopt this kind of presentation.

Assessment Of Dynamic Properties Of A Crowd Model For Human-Structure Interaction Modeling

As lightweight and slender structural elements are more frequently used in the design, large scale structures become more flexible and susceptible to excessive vibrations. To ensure the functionality of the structure, dynamic properties of the occupied structure need to be estimated during the design phase. Traditional analysis method models occupants simply as an additional mass; however, research has shown that human occupants could be better modeled as an additional degree-of- freedom. In the United Kingdom, active and passive crowd models are proposed by the Joint Working Group as a result of a series of analytical and experimental research. It is expected that the crowd models would yield a more accurate estimation to the dynamic response of the occupied structure. However, experimental testing recently conducted through a graduate student project at Bucknell University indicated that the proposed passive crowd model might be inaccurate in representing the impact on the structure from the occupants. The objective of this study is to provide an assessment of the validity of the crowd models proposed by JWG through comparing the dynamic properties obtained from experimental testing data and analytical modeling results. The experimental data used in this study was collected by Firman in 2010. The analytical results were obtained by performing a time-history analysis on a finite element model of the occupied structure. The crowd models were created based on the recommendations from the JWG combined with the physical properties of the occupants during the experimental study. During this study, SAP2000 was used to create the finite element models and to implement the analysis; Matlab and ME¿scope were used to obtain the dynamic properties of the structure through processing the time-history analysis results from SAP2000. The result of this study indicates that the active crowd model could quite accurately represent the impact on the structure from occupants standing with bent knees while the passive crowd model could not properly simulate the dynamic response of the structure when occupants were standing straight or sitting on the structure. Future work related to this study involves improving the passive crowd model and evaluating the crowd models with full-scale structure models and operating data.

Structure-based modeling of head -related transfer functions towards interactive customization of binaural sound systems

One of the most popular techniques for creating spatialized virtual sounds is based on the use of Head-Related Transfer Functions (HRTFs). HRTFs are signal processing models that represent the modifications undergone by the acoustic signal as it travels from a sound source to each of the listener's eardrums. These modifications are due to the interaction of the acoustic waves with the listener's torso, shoulders, head and pinnae, or outer ears. As such, HRTFs are somewhat different for each listener. For a listener to perceive synthesized 3-D sound cues correctly, the synthesized cues must be similar to the listener's own HRTFs. ^ One can measure individual HRTFs using specialized recording systems, however, these systems are prohibitively expensive and restrict the portability of the 3-D sound system. HRTF-based systems also face several computational challenges. This dissertation presents an alternative method for the synthesis of binaural spatialized sounds. The sound entering the pinna undergoes several reflective, diffractive and resonant phenomena, which determine the HRTF. Using signal processing tools, such as Prony's signal modeling method, an appropriate set of time delays and a resonant frequency were used to approximate the measured Head-Related Impulse Responses (HRIRs). Statistical analysis was used to find out empirical equations describing how the reflections and resonances are determined by the shape and size of the pinna features obtained from 3D images of 15 experimental subjects modeled in the project. These equations were used to yield “Model HRTFs” that can create elevation effects. ^ Listening tests conducted on 10 subjects show that these model HRTFs are 5% more effective than generic HRTFs when it comes to localizing sounds in the frontal plane. The number of reversals (perception of sound source above the horizontal plane when actually it is below the plane and vice versa) was also reduced by 5.7%, showing the perceptual effectiveness of this approach. The model is simple, yet versatile because it relies on easy to measure parameters to create an individualized HRTF. This low-order parameterized model also reduces the computational and storage demands, while maintaining a sufficient number of perceptually relevant spectral cues. ^

Structure analysis on the nanoscale : closed WS2 nanoboxes through a cascade of topo- and epitactic processes

Closed WS2 nanoboxes were formed by topotactic sulfidization of a WO3/WO3 center dot 1/3H(2)O intergrowth precursor. Automated diffraction tomography was used to elucidate the growth mechanism of these unconventional hollow structures. By partial conversion and structural analysis of the products, each of them representing a snapshot of the reaction at a given point in time, the overall reaction can be broken down into a cascade of individual steps and each of them identified with a basic mechanism. During the initial step of sulfidization WO3 center dot 1/3H(2)O transforms into hexagonal WO3 whose surface allows for the epitaxial induction of WS2. The initially formed platelets of WS2 exhibit a preferred orientation with respect to the nanorod surface. In the final step individual layers of WS2 coalesce to form closed shells. In essence, a cascade of several topotactic reactions leads to epitactic induction and formation of closed rectangular hollow boxes made up from hexagonal layers.

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet

Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/ PBE/.

Electron diffraction structure analysis: structural research with low-quality diffraction data

Electron Diffraction Structure Analysis (EDSA) with data from standard selected-area electron diffraction (SAED) is still the method of choice for structure determination of nano-sized single crystals. The recently determined heavy atom structure α-Ti2Se (Albe & Weirich, 2003) is used as an example to illustrate the developed procedure for structure determination from two-dimensionally SAED data via direct methods and kinematical least-squares refinement. Despite the investigated crystallite had a relatively large effective thickness of about 230 Å as determined from dynamical calculations, the obtained structural model from SAED data was found in good agreement with the result from an earlier single crystal X-ray study (Weirich, Pöttgen & Simon, 1996). Arguments, which support the validity of the used quasi-kinematical approach, are given in the text. The influences of dynamical and secondary scattering on the quality of the data and the structure solution are discussed. Moreover, the usefulness of first-principles calculations for verifying the results from EDSA is demonstrated by two examples, whereas one of the structures was unattainable by conventional X-ray diffraction.

Variable temperature x-ray crystal structure analysis of a type I langbeinite: Rb2Cd2(SO4)(3)

The structure of a type I langbeinite, Rb2Cd2(SO4)(3), displays three different phases, cubic with a = 10.378(5) Angstrom (space group P2(1)3) at room temperature, monoclinic at 120 K with a = 10.328(3), b = 10.322(3), c = 10.325(3) Angstrom, beta = 89.975(1)degrees (space group P2(1)), and orthorhombic at 85 K with a = 10.319(2), b = 10.321(2), c = 10.320(2) Angstrom (space group P2(1)2(1)2(1)), respectively. Precise single-crystal analyses of these phases indicate that Rb2Cd2(SO4)(3) distorts initially from cubic to monoclinic upon cooling followed by a significant reorientation of the SO4 tetrahedra, resulting in an orthorhombic symmetry upon further cooling. The three structures have been established unequivocally using the same crystal. There is no indication of the formation of an intermediate triclinic phase or any lattice disorder as conjectured in several earlier reports on compounds belonging to the type I langbeinite. The bond valence sum analyses of the coordination around the Rb sites indicate asymmetry in the bond strengths which could be the driving force of the ferroelectric behavior in these materials.

Crystal structure of a beta-prism II lectin from Remusatia vivipara

The crystal structure of a beta-prism II (BP2) fold lectin from Remusatia vivipara, a plant of traditional medicinal value, has been determined at a resolution of 2.4 A. This lectin (RVL, Remusatia vivipara lectin) is a dimer with each protomer having two distinct BP2 domains without a linker between them. It belongs to the ``monocot mannose-binding'' lectin family, which consists of proteins of high sequence and structural similarity. Though the overall tertiary structure is similar to that of lectins from snowdrop bulbs and garlic, crucial differences in the mannose-binding regions and oligomerization were observed. Unlike most of the other structurally known proteins in this family, only one of the three carbohydrate recognition sites (CRSs) per BP2 domain is found to be conserved. RVL does not recognize simple mannose moieties. RVL binds to only N-linked complex glycans like those present on the gp120 envelope glycoprotein of HIV and mannosylated blood proteins like fetuin, but not to simple mannose moieties. The molecular basis for these features and their possible functional implications to understand the different levels of carbohydrate affinities in this structural family have been investigated through structure analysis, modeling and binding studies. Apart from being the first structure of a lectin to be reported from the Araceae/Arum family, this protein also displays a novel mode of oligomerization among BP2 lectins.

Crystal-structure analysis of cis-X-pro-containing peptidomimetics: understanding the steric interactions at cis X-pro amide bonds

Catch the twist: The cis Piv-Pro conformer (Piv=pivaloyl) of peptides is no longer inaccessible. Any cis X-Pro tertiary-amide-bond conformer can be stabilized in crystals of peptides by accommodating the unavoidable distortion of the dihedral angle of the peptide bond to the carbonyl group of the Pro residue (see picture), in this case through ni−1→πi* interactions. Steric clashes were not observed in the cis Piv-Pro rotamers studied.

Use of polydispersity index as control parameter to study melting/freezing of Lennard-Jones system: Comparison among predictions of bifurcation theory with Lindemann criterion, inherent structure analysis and Hansen-Verlet rule

Using polydispersity index as an additional order parameter we investigate freezing/melting transition of Lennard-Jones polydisperse systems (with Gaussian polydispersity in size), especially to gain insight into the origin of the terminal polydispersity. The average inherent structure (IS) energy and root mean square displacement (RMSD) of the solid before melting both exhibit quite similar polydispersity dependence including a discontinuity at solid-liquid transition point. Lindemann ratio, obtained from RMSD, is found to be dependent on temperature. At a given number density, there exists a value of polydispersity index (delta (P)) above which no crystalline solid is stable. This transition value of polydispersity(termed as transition polydispersity, delta (P) ) is found to depend strongly on temperature, a feature missed in hard sphere model systems. Additionally, for a particular temperature when number density is increased, delta (P) shifts to higher values. This temperature and number density dependent value of delta (P) saturates surprisingly to a value which is found to be nearly the same for all temperatures, known as terminal polydispersity (delta (TP)). This value (delta (TP) similar to 0.11) is in excellent agreement with the experimental value of 0.12, but differs from hard sphere transition where this limiting value is only 0.048. Terminal polydispersity (delta (TP)) thus has a quasiuniversal character. Interestingly, the bifurcation diagram obtained from non-linear integral equation theories of freezing seems to provide an explanation of the existence of unique terminal polydispersity in polydisperse systems. Global bond orientational order parameter is calculated to obtain further insights into mechanism for melting.

Structure analysis of the SECRAL superconducting magnet system

An advanced superconducting ECR ion source named SECRAL has been constructed at Institute of Modern Physics of Chinese Academy of Sciences, whose superconducting magnet assembly consists of three axial solenoid coils and six sextupole coils with a cold iron structure as field booster and clamp. In order to investigate the structure of sextupole coils and to increase the structural reliabilities of the magnet system, global and local structural analysis have been performed in various operation scenarios. Winding pack and support structure design of magnet system, mechanical calculation and stress analysis are given in this paper. From the analysis results, it has been found that the magnet system is safe in the referential operation scenarios and the configuration of the magnet complies with design requirements of the SECRAL.