排序方式: 共有51条查询结果,搜索用时 15 毫秒
41.
42.
Sery Gonedelé Bi Didier P Sokouri Kouakou Tiékoura Oulo Alla N?Nan Marcel Lolo Félix Gnangbé Assanvo SP N?Guetta 《Bioinformation》2014,10(11):671-678
Cête d׳Ivoire continues to have the highest HIV-1 prevalence rate in West Africa, although the infection number is in constant decline. The external envelope protein of the viruses is a likely site of selection, and responsible for receptor binding and entry into host cells, and therefore constitutes an ideal region with which to investigate the evolutionary processes acting on HIV-1. In this study, we analyse 189 envelope glycoprotein V3 loop region sequences of viruse isolates from 1995 to 2009, from HIV-1 untreated patients living in Cête d׳Ivoire, to decipher the temporal relationship between disease diversity, divergence and selection. Our analyses show that the nonsynonymous and synonymous ratio (dN/dS) was lower than 1 for viral populations analysed within 15 years, which showed the sequences did not undergo adequate immune pressure. The phylogenetic tree of the sequences analysed demonstrated distinctly long internal branches and short external branches, suggesting that only a small number of viruses infected the new host cell at each transmission. In addition to identifying sites under purifying selection, we also identified neutral sites that can cause false positive inference of selection. These sites presented form a resource for future studies of selection pressures acting on HIV-1 enν gene in Cête d׳Ivoire and other West African countries. 相似文献
43.
Oliver Beckstein Ekaterina Ivanova Tian Geng Simone Weyand David Drew Joseph Lanigan David J Sharples Mark SP Sansom So Iwata Colin WG Fishwick A Peter Johnson Alexander D Cameron Peter JF Henderson 《The EMBO journal》2014,33(16):1831-1844
The hydantoin transporter Mhp1 is a sodium‐coupled secondary active transport protein of the nucleobase‐cation‐symport family and a member of the widespread 5‐helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site‐directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5‐substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5‐substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5‐(2‐naphthylmethyl)‐L‐hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1. 相似文献
44.
DOMINIK LERMEN BRUNHILDE BLÖMEKE ROBERT BROWNE ANN CLARKE PAUL W. DYCE THOMAS FIXEMER GÜNTER R. FUHR WILLIAM V. HOLT KATARINA JEWGENOW RHIANNON E. LLOYD STEFAN LÖTTERS MARTIN PAULUS GORDON MCGREGOR REID DANIEL H. RAPOPORT DAVID RAWSON JENNIFER RINGLEB OLIVER A. RYDER GABRIELE SPÖRL THOMAS SCHMITT MICHAEL VEITH PAUL MÜLLER 《Molecular ecology》2009,18(6):1030-1033
Cryobanking, the freezing of biological specimens to maintain their integrity for a variety of anticipated and unanticipated uses, offers unique opportunities to advance the basic knowledge of biological systems and their evolution. Notably, cryobanking provides a crucial opportunity to support conservation efforts for endangered species. Historically, cryobanking has been developed mostly in response to human economic and medical needs — these needs must now be extended to biodiversity conservation. Reproduction technologies utilizing cryobanked gametes, embryos and somatic cells are already vital components of endangered species recovery efforts. Advances in modern biological research (e.g. stem cell research, genomics and proteomics) are already drawing heavily on cryobanked specimens, and future needs are anticipated to be immense. The challenges of developing and applying cryobanking for a broader diversity of species were addressed at an international conference held at Trier University (Germany) in June 2008. However, the magnitude of the potential benefits of cryobanking stood in stark contrast to the lack of substantial resources available for this area of strategic interest for biological science — and society at large. The meeting at Trier established a foundation for a strong global incentive to cryobank threatened species. The establishment of an Amphibian Ark cryobanking programme offers the first opportunity for global cooperation to achieve the cryobanking of the threatened species from an entire vertebrate class. 相似文献
45.
46.
47.
Saravana Prakash Thirumuruganandham Herbert M. Urbassek 《Journal of molecular modeling》2009,15(8):959-969
Vibrational excitations of low-frequency collective modes are essential for functionally important conformational transitions
in proteins. We carried out an analysis of the low-frequency modes in the G protein coupled receptors (GPCR) family of cone
opsins based on both normal-mode analysis and molecular dynamics (MD) simulations. Power spectra obtained by MD can be compared
directly with normal modes. In agreement with existing experimental evidence related to transmembrane proteins, cone opsins
have functionally important transitions that correspond to approximately 950 modes and are found below 80 cm−1. This is in contrast to bacteriorhodopsin and rhodopsin, where the important low-frequency transition modes are below 50 cm−1. We find that the density of states (DOS) profile of blue opsin in a solvent (e.g. water) has increased populations in the
very lowest frequency modes (<15 cm−1); this is indicative of the increased thermostability of blue opsin. From our work we found that, although light absorption
behaves differently in blue, green and red opsins, their low-frequency vibrational motions are similar. The similarities and
differences in the domain motions of blue, red and green opsins are discussed for several representative modes. In addition,
the influence of the presence of a solvent is reported and compared with vacuum spectra. We thus demonstrate that terahertz
spectroscopy of low-frequency modes might be relevant for identifying those vibrational degrees of freedom that correlate
to known conformational changes in opsins.
An erratum to this article can be found at 相似文献
48.
49.
50.