Molecular dynamics of human alpha-fetoprotein fragment LDSYQCT and its analogs at different dielectric constants

A comparative study of the conformation dynamics of the human alpha-fetoprotein fragment LDSYQCT and heptapeptides derived from it by point substitutions has revealed a significant influence of electrostatic interactions on the set of preferred conformations and dynamics of amino acid residues when the peptides with blocked termini are examined at ? = 1. Peptide flexibility rises when the termini are left free (charged). At ? = 10 or 80, the set of probable conformations for all residues expands to much the same extent, i.e., at higher permittivity of the medium the dynamic effects of amino acid changes are leveled off.     

不受欢迎的生物多样性：香港的外来植物物种

香港早在19世纪中叶开始就有外来植物入侵的记录,迄今为止,已发现多达238种已归化的外来或怀疑为外来的植物,其中又以薇甘菊（Mikania micrantha)、五爪金龙（Ipomoea cairica)、假臭草（Eupatorium catarium)、大黍（Panicum maximum)等最常见,外来植物最常见于受人为干扰的生境,例如荒废农田及路旁等,而较少在天然林地生境及贫瘠的灌草丛中发现,外来植物的对本地生态系统的影响主要局限于低地生境,它们常形成单优种群,减少了生境及贫瘠的灌草丛中发现,外来植物对本地生态系统的影响主要局限于低地生境,它们常形成单优种群,减少少了生境及动植物的多样性,外来动物对香港原生植物影响最大的是于20世纪70年代入侵的松树线虫（Bur-saphelenchus xylophilus)。外来的脊椎动物也有可能对香港的植物被演替产生影响,目前香港的外来植物当中,有些在大陆较少分布或没有记录,作为华南最大的港口,香港对外来物种的引入扮演着重要的角色,因此制定控制外来种在香港及华南地区的引入及传播的政策及措施非常重要。     

Cell adhesion proteins and α-fetoprotein. Similar structural motifs as prerequisites for common functions

This review summarizes and analyzes data on structural and functional relationships between cell adhesion proteins and alpha-fetoprotein (AFP), which play an important role in embryo- and carcinogenesis and act in synergism with growth factors. These two groups of proteins are mosaic, multimodular, and polyfunctional, and each of their modules can function independently through binding with its specific membrane receptor. Most cell adhesion proteins contain modules similar to epidermal growth factor (EGF) and also their repeats, which determine the involvement of these proteins in regulation of cell proliferation, differentiation, and apoptosis. These EGF-like modules are found to include short motifs similar to the fragment LDSYQCT of human AFP. Both direct and inverted AFP-like motifs are linked through a consensus octapeptide motif CXXGY/FXGX. Such AFP-like motifs of cell adhesion proteins and the tripeptide RGD found in AFP may be structural prerequisites for common functions of these groups of nonhomologous and unrelated proteins.     

A molecular dynamics simulation study of human alpha-fetoprotein-derived peptide and its analogues. Influence of dielectric constant

A comparative study of the conformation dynamics of a series of heptapeptides: the human alpha-fetoprotein fragment LDSYQCT and its seven analogues has been conducted. The effect of the dielectric constant of medium on the dynamics of heptapeptide conformation is considered. It is shown that electrostatic interactions have a marked effect on several accessible conformations and the dynamics of the behavior of amino acid residues.     

Competitive affinity chromatography of human alpha fetoprotein on immobilized diethylstilbestrol]

Human alpha-fetoprotein (AFP) was isolated by affinity chromatography method on immobilized diethylstilbestrol from butanol extract of abortive material. Elution from the column was performed with 10% aqueous buffered butanol solution, pH 8.6. During one procedure human AFP-preparation containing about 10% of AFP and about 90% of albumin was obtained, with the yield about 60%. The preliminary incubation of extract of the abortive material with estrone raised AFP yield up to 85% with the increase of AFP content in the preparation up to 35%, and preincubation with estriol and estradiol caused the increase of the yield up to 88-92%, and AFP content in the preparation was 50% and 65%, respectively. The preincubation of human AFP with diethylstilbestrol lowers the yield of this protein, which testified to the possible binding of human AFP with free diethylstilbestrol; testosterone, hydrocortisone and desoxycorticosterone caused the increase of the yield of AFP. So the competitive variant of the affinity chromatography on immobilized diethylstilbestrol makes it possible to raise human AFP preparation purity and yield by decreasing the competition between AFP, and not binding free steroid hormones, ad albumin for immobilized diethylstilbestrol.     

Influence of intramolecular interactions on conformational and dynamic properties of analogs of heptapeptide AFP<Subscript>14–20</Subscript>

Conformational and dynamic properties of proteins and peptides play an important role in their functioning. However, mechanisms that underlie this influence have not been fully elucidated. In the present work we computationally constructed analogs of heptapeptide AFP_14–20 (LDSYQCT) — one of the biologically active sites of human α-fetoprotein (AFP) — to study their conformational and dynamic properties using molecular dynamics simulation. Analogs were obtained by point substitutions of amino acid residues taking into account differences in their physicochemical properties and also on the basis of analysis of amino acid substitutions in the AFP_14–20-like motifs revealed in different physiologically active proteins. It is shown that changes in conformational mobility of amino acid residues of analogs are due to disruption or arising of intramolecular interactions that, in turn, determine existence of steric restrictions during rotation around covalent bonds of the peptide backbone. Substitution of an amino acid by another one with significant difference in physicochemical properties may not lead to remarkable changes in conformational and dynamic properties of the peptide if intramolecular interactions remain unchanged.     

Structural and functional mapping of α-fetoprotein

Alpha-fetoprotein (AFP) is a major mammalian oncofetal protein, which is also present in small quantities in adults. It is a member of the albuminoid gene superfamily, which consists of AFP, serum albumin, vitamin D binding protein, and alpha-albumin (afamin). Although physicochemical and immunological properties of AFP have been well-studied, its biological role in embryo- and carcinogenesis and in adult organisms as well as mechanisms underlying its functioning remain unclear. During the recent decades, the biological role of AFP has been evaluated by identification of its functionally important sites. Comparison of primary structure of AFP and some physiologically active proteins revealed similarity of some polypeptide regions. This has been used for prediction of AFP functions (i.e., its multifunctionality). Localization of functionally important sites followed by determination of their amino acid composition and type of biological activity has provided valuable information for structural-functional mapping of AFP. Some peptide fragments of AFP have been synthesized and tested for biological activity. This review summarizes data on structural-functional interrelationships. We also describe functionally important AFP sites found by various groups during the last decade of structural-functional mapping of AFP with experimentally confirmed and putative biologically active sites.     

Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana

To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the possibility that dimorphic DNA variation exists in the entire nuclear genome of A. thaliana. The ChiA region was divided into two blocks by an intragenic recombination between two parental sequence types, which diverged 7.4 MYA under the assumption that nucleotide mutation rate per site per year is mu = 10(- 9). Nucleotide diversity in the entire ChiA region was 0.0104. Tajima's test was significantly negative for both nucleotide and indel variations, which was manifested as an excess of unique polymorphisms. However, the level and pattern of polymorphism in the ChiA region were inconsistent with simple theoretical explanations. The HKA test detected no difference in the levels of intra- and interspecific variations between the ChiA and Adh regions. In the ChiA coding region, no difference in the patterns of synonymous and replacement variation was found in intra- and interspecific comparisons by the MK test. Although it was difficult to determine the exact genetic mechanism acting on the ChA locus, these results suggested that the ChA locus region was under the same genetic mechanism before and after the establishment of A. thaliana as a species.      

Affinity chromatography of mouse and rat alpha-fetoproteins on immobilized diethylstilbestrol]

Alpha-fetoproteins (AFP) from amniotic fluid of mouse and rat demonstrate high affinity and specificity during their binding with immobilized diethylstilbestrol, which allows to isolate these two proteins by one step using the method of affinity chromatography on Sepharose with immobilized diethylstilbestrol. Meanwhile the yield of mouse AFP was 42%, and rat AFP--75%. The preliminary incubation of the amniotic fluid of rat and mouse with free estradiol results in abrupt fall of AFP outcome, which may testify to the binding of estradiol and diethylstilbestrol by the same receptor sites on AFP molecule.