Biomedical subjects

Yanli Wang

Publications and source records attributed to Yanli Wang.

27 records · Page 2Linked to original sources

PubMed2004

Insight into the structural role of carotenoids in the photosystem I: a quantum chemical analysis.

The structural stabilization role of carotenoids in the formation of photosynthetic pigment-protein complexes is investigated theoretically. The pi-pi stacking and CH-pi interactions between beta-carotenes and their surrounding chlorophylls (and/or aromatic residues) in Photosystem I (PS1) from the cyanobacterium Synechococcus elongatus were studied by means of the supermolecular approach at the level of the second-order Møller-Plesset perturbation method. PS1 features a core integral antenna system consisting of 22 beta-carotenes intertwined with 90 chlorophyll molecules. The binding environments of all 22 beta-carotenes were systematically analyzed. For 21 out of the 22 cases, one or more chlorophyll molecules exist within van der Waals' contacts of the beta-carotene molecule. The calculated strengths of pi-pi stacking interactions between the conjugated core of beta-carotene and the aromatic tetrapyrrole rings of chlorophyll are substantial, ranging from -3.54 kcal/mol for the perpendicular-positioned BCR4004...CHL1217 pair to -16.01 kcal/mol for the parallel-oriented BCR4007...CHL1122 pair. A strong dependence of the pi-pi stacking interaction energies on the intermolecular configurations of the two interacting pi-planes is observed. The parallel-oriented beta-carotene and chlorophyll pair is energetically much more stable than the perpendicular-positioned pair. The larger the extent of pi-pi overlapping, the stronger the interaction strength. In many cases, the beta-ring ends of beta-carotene molecules are found to interact with the tetrapyrrole rings of chlorophyll via CH-pi interactions. For the latter interactions, the calculated interaction strengths vary from -7.03 to -11.03 kcal/mol, depending on the intermolecular configuration. This work leads to the conclusion that pi-pi stacking and CH-pi interactions between beta-carotene and their surrounding chlorophylls and aromatic residues play an essential role in binding beta-carotenes in PS1 from S. elongatus. Consequently, the molecular basis of the structural stabilization function of carotenoids in formation of the photosynthetic pigment-protein complexes is established.

Biophysics↗

PubMed2004

[Effect of chronic abacterial prostatitis on semen quality and efficacy of antibacterial agents].

OBJECTIVE: To appraise the effect of chronic abacterial prostatitis (CAP) on semen quality and the efficacy of antibacterial agents. METHODS: The semen of 86 cases of CAP and 20 normal men were analysed together with the antisperm antibodies in their blood and semen, and the antisperm antibodies in the blood and spermatic fluid were determined. Then the 86 patients were randomized into two groups, one treated with Chinese traditional medicine, indomethacin and three kinds of antibacterial agents, the other with Chinese traditional medicine and indomethacin only. The treatment lasted 3 months, and a follow-up visit was paid every month. RESULTS: Sperm motility and normal modality of the CAP group were 59.8% and 52.8%, respectively, significantly lower than those of the normal group (P < 0.005). The positive rates of the antisperm antibodies in the blood and spermatic fluid were 46.5% and 50%, respectively, significantly higher than those of the normal group. The clinical efficacy was significantly better in the group treated with antibacterial agents than the one without (P < 0.05). CONCLUSION: CAP can affect sperm quality and decrease fertility. Antibacterial agents can obviously enhance sperm quality and the cure rate of CAP.

Adolescent↗

PubMed2003

Multiple intermolecular interaction modes of positively charged residues with adenine in ATP-binding proteins.

Adenosine 5'-triphosphate (ATP) plays an essential role in all forms of life. Molecular recognition of ATP in ATP-binding proteins is a subject of great importance for understanding enzymatic mechanisms and for drug design. We have carried out a large-scale data mining of the Protein Data Bank (PDB) to analyze molecular determinants for recognition of ATP, in particular, the adenine base, by ATP-binding proteins. A novel distribution pattern of charged residues around the adenine base was discovered: lysine residues tend to occupy the major groove N7 side of the adenine base, and the arginine residues situate preferentially above or below the adenine bases. Such an arrangement is advantageous because it facilitates multiple modes of intermolecular interactions, that is, cation-pi interactions and a hydrogen bond between lysine and adenine, and cation-pi and pi-pi stacking interactions between arginine and adenine. For the two representative Lys... Adenine and Arg... Adenine interactions, intermolecular interaction energies were subsequently analyzed by means of the supermolecular approach at the MP2 level with solvation free energy correction using the SM5.42R model of Cramer and Truhlar, which gave rise to significant interaction strengths.

Adenine↗

PubMed2003

Loss of integrin alpha(v)beta6-mediated TGF-beta activation causes Mmp12-dependent emphysema.

Integrins are heterodimeric cell-surface proteins that regulate cell growth, migration and survival. We have shown previously that the epithelial-restricted integrin alpha(v)beta6 has another critical function; that is, it binds and activates latent transforming growth factor-beta (TGF-beta). Through a global analysis of pulmonary gene expression in the lungs of mice lacking this integrin (Itgb6 null mice) we have identified a marked induction of macrophage metalloelastase (Mmp12)--a metalloproteinase that preferentially degrades elastin and has been implicated in the chronic lung disease emphysema. Here we report that Itgb6-null mice develop age-related emphysema that is completely abrogated either by transgenic expression of versions of the beta6 integrin subunit that support TGF-beta activation, or by the loss of Mmp12. Furthermore, we show that the effects of Itgb6 deletion are overcome by simultaneous transgenic expression of active TGF-beta1. We have uncovered a pathway in which the loss of integrin-mediated activation of latent TGF-beta causes age-dependent pulmonary emphysema through alterations of macrophage Mmp12 expression. Furthermore, we show that a functional alteration in the TGF-beta activation pathway affects susceptibility to this disease.

Aging↗

PubMed2003

Convenient synthesis of polyfunctionalized beta-fluoropyrroles from rhodium(II)-catalyzed intramolecular N-H insertion reactions.

Polyfunctionalized beta-fluoropyrrole can be readily prepared from rhodium(II) acetate-catalyzed intramolecular N-H insertion reaction of delta-amino-gamma,gamma-difluoro-alpha-diazo-beta-ketoesters. A cyanomethylene group can be introduced at C-3 of the pyrrole ring through the Wittig reaction of the diazo compounds followed by rhodium(II)-catalyzed intramolecular N-H insertion reactions.

Catalysis↗

PubMed2003

MMDB: Entrez's 3D-structure database.

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html.

Animals↗

PubMed2003

CDD: a curated Entrez database of conserved domain alignments.

The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi.nlm.nih.gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.

Amino Acid Sequence↗

PubMed2002

A quantum chemistry study of binding carotenoids in the bacterial light-harvesting complexes.

Carotenoids play the dual function of light harvesting and photoprotection in photosynthetic organisms. Despite their functional importance, the molecular basis for binding of carotenoids in the photosynthetic proteins is poorly understood. We have discovered that all carotenoids are surrounded either by aromatic residues or by chlorophylls in all known crystal structures of the photosynthetic pigment-protein complexes. The intermolecular pi-pi stacking interactions between carotenoids and the surrounding aromatic residues in the light-harvesting complex II (LH-II) of Rhodospirillum molischianum were analyzed by high level ab initio electronic structure calculations. Intermolecular interaction energies were calculated with the second-order Møller-Plesset perturbation method (MP2) using the modified 6-31G*(0.25) basis set with diffuse d-polarization by Hobza and co-workers. The MP2/6-31G*(0.25) calculations yield a total stabilization energy of -15.66 kcal/mol between the carotenoid molecule and the four surrounding aromatic residues (alpha-Trp-23, beta-Phe-20, beta-Phe-24, beta-Phe-27). It is thus concluded that pi-pi stacking interactions between carotenoids and the aromatic residues play an essential role in binding carotenoids in the LH-II complex of Rhodospirillum molischianum. The physical nature of the pi-pi stacking interactions was further analyzed, and the dispersion interactions were found to be the dominant intermolecular attraction force. There is also a substantial electrostatic contribution to the overall intermolecular stabilization energy.

Carotenoids↗

PubMed2002

MMDB: Entrez's 3D-structure database.

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez's 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez's search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez's Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure.

Animals↗