Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

Discovery of genes involved in defense/immunity functions in a haemocytes cDNA library from Fenneropenaeus chinensis by ESTs annotation

Crustacean haemocytes play important roles in the host immune response including recognition, phagocytosis, melanization, cytotoxicity and inter-cellular signal communication. Expressed sequence tags (ESTs) analysis is proved to be an efficient approach not only for gene discovery, but also for gene expression profiles performance. In order to further understand the innate immune system and defense mechanisms of Chinese shrimp at molecular level, complementary DNA library is constructed from the haemocyte tissue of Fenneropenaeus chinensis. A total of 2371 cDNA clones are successfully sequenced and the average sequence length is 460 bp. About 50% are identified as orthologs of known genes from other organisms by BLASTx and BLASTn program. By sequences comparability and analysis, 34 important genes including 177 ESTs are identified that may be involved in defense or immune functions in shrimp based on the known knowledge. These genes are categorized into five categories according to their putative functions in shrimp immune system: 13 genes are different types of antimicrobial peptides (AMP, penaeidin, antilipopolysaccharide factor, etc.), and their proportion is about 3 8%; 11 genes belong to prophenoloxidase system (prophenoloxidase, serine proteinase, serine proteinase inhibitor, etc.), and their proportion is about 32%; five genes have high homology with clotting protein (lectin, transglutaminase, etc), and their proportion is about 15%; three genes may be involved in inter-cell signal communication (peroxinectin, integrin), and their proportion is about 9%; two genes have been identified to be chaperone proteins (Hsc70, thioredoxin peroxidase), and their proportion is about 6%. These EST sequences enrich our understanding of the immune genes of F chinensis and will help farther experimental research into immune factors and improve our knowledge of the immune mechanisms of shrimp. (c) 2007 Elsevier B.V. All rights reserved.

Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria

Cyclic nucleotides (both cAMP and cGMP) play extremely important roles in cyanobacteria, such as regulating heterocyst formation, respiration, or gliding. Catalyzing the formation of cAMP and cGMP from ATP and GTP is a group of functionally important enzymes named adenylate cyclases and guanylate cyclases, respectively. To understand their evolutionary patterns, in this study, we presented a systematic analysis of all the cyclases in cyanobacterial genomes. We found that different cyanobacteria had various numbers of cyclases in view of their remarkable diversities in genome size and physiology. Most of these cyclases exhibited distinct domain architectures, which implies the versatile functions of cyanobacterial cyclases. Mapping the whole set of cyclase domain architectures from diverse prokaryotic organisms to their phylogenetic tree and detailed phylogenetic analysis of cyclase catalytic domains revealed that lineage-specific domain recruitment appeared to be the most prevailing pattern contributing to the great variability of cyanobacterial cyclase domain architectures. However, other scenarios, such as gene duplication, also occurred during the evolution of cyanobacterial cyclases. Sequence divergence seemed to contribute to the origin of putative guanylate cyclases which were found only in cyanobacteria. In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications.

On SAR wind speed ambiguities and related geophysical model functions

Recent investigations show that normalized radar cross sections for C-band microwave sensors decrease under high wind conditions with certain incident angles instead of increase, as is the case for low to moderate wind speeds. This creates the problem of ambiguities in high wind speed retrievals from synthetic aperture radar (SAR). In the present work, four geophysical model functions (GMFs) are studied, namely the high wind C-band model 4 (CMOD4HW), C-band model 5 (CMOD5), the high wind vertical polarized GMF (HWGMF_VV), and the high wind horizontal polarized GMF (HWGMF_HH). Our focus is on model behaviours relative to wind speed ambiguities. We show that, except for CMOD4HW, the other GMFs exhibit the wind speed ambiguity problem. To consider this problem in high wind speed retrievals from SAR, we focus on hurricanes and propose a method to remove the speed ambiguity using the dominant hurricane wind structure.

Forms and functions of inorganic carbon in the Jiaozhou Bay sediments

Inorganic carbon forms and their influencing factors, mutual transformation and contribution to carbon cycling in the Jiaozhou Bay sediments were discussed. The results show that inorganic carbon in sediments could be divided into five forms: NaCl form, NH3 center dot H2O form, NaOH form, NH2OH center dot HCl form and HCl form. Thereinto, NH2OH center dot HCl form and HCl form account for more than 70% of total inorganic carbon. There was close relationship among every form of inorganic carbon and their correlativity was clearly different with different sedimentary environment except the similar strong positive correlation among NH2OH center dot HCl form, HCl form and total inorganic carbon in all regions of the Jiaozhou Bay. All forms of inorganic carbon were influenced by organic carbon, pH, Eh, Es, nitrogen and phosphorus in sediments, but their influence had different characteristics in different regions. Every farm of inorganic carbon transformed into each other continuously during early diagenesis of sediments and the common phenomenon was that NaCl form, NH3 center dot H2O form, NaOH form and NH2OH center dot HCl form might transform into steady HCl form. NaCl form, NH3 center dot H2O form, NaOH form and NH2OH center dot HCl form could participate in carbon recycle and they are potential carbon source; HCl form may be buried for a long time in sediments, and it may be one of the final resting places of atmospheric CO2. Inorganic carbon which entered into sediments was about 4.98 x 10(10) g in the Jiaozhou Bay every year, in which about 1.47x10(10) g of inorganic carbon might be buried for a long time and about 3.51. x 10(10) g of inorganic carbon might return into seawater and take part in carbon recycling.

A set of polymorphic microsatellite loci for the bay scallop, Argopecten irradians

The method of creating enriched microsatellite libraries can supply an abundant source of microsatellite sequences at a considerably reduced cost. Here we report the development of 15 polymorphic microsatellite loci from the bay scallop, Argopecten irradians, using enrichment protocol. Polymorphism was assessed in a sample of hatchery population (n = 38) revealing three to seven alleles per locus. The expected and observed heterozygosities ranged from 0.198 to 0.813 and from 0.083 to 0.833, respectively. These markers will be useful for genetic variation monitoring and parentage analysis.