5SRNA二级结构的研究 1.一种以Fox模型为基础的微型计算机方法

本文系以Fox模型为兰本而设计的一种建立5S RNA二级结构的微型计算机方法。将5S RNA分子的核苷酸顺序作为信息输入,经Z—80微型计算机处理约4分钟后,即可建立在仅考虑二级相互作用的情况下,相当于Fox模型的具有最低自由能的二级结构。本方法获得的结果与同样以Fox模型为兰本的其它方法所得到的结果相符。本方法简便、快速和费用低廉,易于推广应用。

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin(HA)cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes.We have developed a dynamic extended folding strategy to predict RNA secondary structure with RNAstructure 4.1 program in an iterative extension process.Statistical analysis of the sequences showed that the HA cleavage site basic amino acids favor the adenine-rich codons,and the corresponding mRNA fragments are mainly in the folding states of single-stranded loops.Our sequential and structural analyses showed that to prevent and control these highly pathogenic viruses,that is,to inhibit the gene expression of avian influenza virus H5N1 subtypes,we should consider the single-stranded loop regions of the HA cleavage site-coding sequences as the targets of RNA interference.

Physicochemical bases for protein folding,dynamics,and protein-ligand binding

Proteins are essential parts of living organisms and participate in virtually every process within cells.As the genomic sequences for increasing number of organisms are completed,research into how proteins can perform such a variety of functions has become much more intensive because the value of the genomic sequences relies on the accuracy of understanding the encoded gene products.Although the static three-dimensional structures of many proteins are known,the functions of proteins are ultimately governed by their dynamic characteristics,including the folding process,conformational fluctuations,molecular motions,and protein-ligand interactions.In this review,the physicochemical principles underlying these dynamic processes are discussed in depth based on the free energy landscape(FEL)theory.Questions of why and how proteins fold into their native conformational states,why proteins are inherently dynamic,and how their dynamic personalities govern protein functions are answered.This paper will contribute to the understanding of structure-function relationship of proteins in the post-genome era of life science research.

Molecular motions and conformational transition between different conformational states of HIV-1 gp120 envelope glycoprotein

The HIV-1 gp120 exterior envelope glycoprotein undergoes a series of conformational rearrangements while sequentially interacting with the receptor CD4 and coreceptor CCR5 or CXCR4 on the surface of host cells to initiate virus entry. Both the crystal structures of the HIV-1 gp120 core bound by the CD4 and antigen 17b and the SIV gp120 core pre-bound by CD4 are known. Despite the wealth of knowledge on these static snapshots of molecular conformations,the details of molecular motions involved in conformational transition that are crucial to intervention remain elusive. We presented comprehensive comparative analyses of the dynamics behaviors of the gp120 in its CD4-complexed,CD4-free and CD4-unliganded states based on the homology models with modeled V3 and V4 loops by means of CONCOORD computer simulation to generate ensembles of feasible protein structures that were sub-sequently analysed by essential dynamics analyses to identify preferred concerted motions. The re-vealed collective fluctuations are dominated by complex modes of combinational motions of the rota-tion/twisting,flexing/closure,and shortness/elongation between or within the inner,outer,and bridg-ing-sheet domains,and these modes are related to the CD4 association and HIV neutralization avoid-ance. Further essential subspace overlap analyses were performed to quantitatively distinguish the preference for conformational transitions between the three states,revealing that the unliganded gp120 has a greater potential to translate its conformation into the conformational state adopted by the CD4-complexed gp120 than by the CD4-free gp120,whereas the CD4-free gp120 has a greater potential to translate its conformation into the unliganded state than the CD4-complexed gp120 does. These dynamics data of gp120 in its different conformations are helpful in understanding the relationship between the molecular motion/conformational transition and the function of gp120,and in gp120-structure-based subunit vaccine design.

Relationships of mRNA-protein secondary structures in the human β-globin gene HBB and four variants

Single nucleotide polymorphism is an interesting problem that can alter gene expression,recode amino acids and affect protein function.Protein structural changes have generally been attributed to amino acid replacements,and only a few research efforts have examined the effects of mRNA structural changes to the conformation of the corresponding protein coded by the mRNA.In the present study,the human β-globin HBB gene and four variants were examined.The mRNA secondary structures were constructed using the dynamic extended folding method and the encoded protein secondary structures were obtained from related databases.Comparisons were performed between these structures before and after mutations were introduced into the mature mRNAs and the proteins.We focused on the structural changes from mRNA to protein and found that regular protein conformations tend to match stable mRNA regions,whereas irregular protein conformations,such as β/γ turns and random coils,often match unstable mRNA regions.Mutations within unstable regions can alter the mRNA secondary structure and leave footprints in the protein structure.Comparison of the mRNA-protein secondary structure relationships represents a potential strategy to explore protein functional changes.

Splicing Signals in the Human Hemoglobin Genes at the Sequence and Folding Levels

Identification of the splice sites is a critical and tough issue in eukaryotic genome annotation. Here, a statistical study is introduced for detecting the splicing signals in the human hemoglobin （Hb） pre-mRNAs by using the approaches of regional pairwise alignment, splicing weight matrix scoring, and dynamic extended folding. First, the regional pairwise alignment results show that the coding regions of the human Hb genes are at a high level for both conservation and fluctuation. Second, the weighted matrix scoring results indicate that, although the authentic splicing motifs are always scored the highest in a sequence, the sequence motif alone is inadequate to precisely define the splice sites. Finally, we deduce the RNA frame structures by applying an extended folding approach to analyze the stable folding elements. We find out that the splice sequences tend to take stretching and partially paired conformations, which benefit recognition and competitive binding of the splicing factors. These results indicate that precise splicing is an integrated effect of multiple mechanisms of signal recognition at the level of sequence and structure.