基于氨基酸位置特异性的蛋白质Loop区结构预测改进方法

蛋白质loop区的结构预测是理解蛋白质功能的重要一环,而长loop区的结构预测至今还是生物信息学中的难题.目前己经出现了多种loop结构的算法,其中LEAP是预测精度最高的算法之一,但它在长loop区初始主链构象采样上仍有较大的改进余地.本文中我们将蛋白质二级结构预测算法SPINE X与LEAP算法结合起来,构建了新的主链扭转角分布图(拉氏图),在主链初始构象采样中引入氨基酸在蛋白序列中的位置特异性信息,使得初始构象的采样更具针对性,对取自CASP10单链蛋白的loop测试集的分析表明,对长度为10,11,12个氨基酸的长loop区,改进后算法都比原始LEAP算法的预测精度有显著提升.这种引入氨基酸位置特异性从而提高预测精度的思路有望进一步推广至loop结构预测的其他算法.     

ADSORPTION BEHAVIOR OF AMINO ACIDS ON COPPER SURFACES

The major results of a series of our recent investigations on the adsorption of eight amino acids on Cu(001) and (111) surfaces are reviewed in the present paper. In all studied cases the molecules adsorb onto the surface in their anionic form. With the increase of the coverage three different 2D phases of the adsorbates, that is, the 2D lattice gas, intermediate, and solid phases, appear sequentially, although for few systems one or two of them do not appear. In both the 2D lattice gas and intermediate phases the molecules "stand" with their two oxygen "feet" on the surface and the intermolecular interactions are repulsive, although in the former they can diffuse frequently whereas in the latter they are discommensurate in one direction with the substrate. In the solid phase the molecules "lie" down on the surface to form commensurate superstructures. Adsorption of amino acids may often induce step faceting as well as bunching to form facets. Adsorption of L-lysine on Cu(001) may cause steps bunching to form facets with all the same chirality. Our preliminary results show that it is possible to manipulate individual molecules with the STM tip even at room temperature. These results may have applications in nano-materials, nano-technology, and very likely also in chiral separations or enantioselective heterogeneous catalysis.     

Combined effects of high pressure and sodium hydrogen carbonate treatment on pork ham: improvement of texture and palatability

In this study, the combined effects of high pressure and sodium hydrogen carbonate (NaHCO₃) treatment on the physical and chemical properties, and palatability of pork ham, a tough and under-utilized meat, were investigated. Assessment of meat properties with heat treatment, after exposure to NaHCO₃ and high pressure treatment, revealed an increase in water content, and decreased weight reduction and rupture stress. The free amino acid content of meat samples increased with NaHCO₃ and high pressure treatment. The effect of high pressure processing was especially notable at a pressure of 300 MPa. Sensory evaluation showed that meat subjected to high pressure processing after NaHCO₃ treatment was tender and juicy. In addition, the sample produced minimal residue in the mouth and was characterized by a good taste.     

NMR Studies of Drugs. Applications of Achiral and Chiral Lanthanide Shift Reagents to the Analgesic,Famprofazone: “Anomalous Shifts”

The 200 MHz ¹H NMR spectra of the analgesic, famprofazone, 1, have been studied in CDCl₃ solution at ambient temperatures with the achiral lanthanide shift reagent (LSR) tris (6, 6, 7, 7, 8, 8, 8-heptaf luoro-2, 2-dimethyl-3, 5-octanedionato) europium (III), Eu(FOD)₃, 2, for spectral simplification, and with the chiral LSR, tris [3-(heptafluoropropylhydroxymethylene) - (+) camphorato] europium (III), Eu (HFC)₃, 3. Lanthanide induced shift (LIS) magnitudes suggested predominant LSR binding at the carbonyl oxygen. Substantial enantiomeric shift differences were observed for several nuclei of 1 with added 3 which could permit direct determinations of enantiomeric excess.     

Reminiscence of 40-year research on nitrogen metabolism

This article summarizes my research over 40 years. The main theme of my work is nitrogen metabolism of amino acids, though later I focused on protein turnover in the cell. In the first years of my research work, I was busy dissecting the pathways involved in the metabolism of certain amino acids and their related enzymes. Then I became interested in the physiology and regulation of matabolism of these amino acids. For that, I used primary cultured hepatocytes, which contain many liver-specific enzymes. However, this play field was very rough around 1970 and hence I had to smooth them (differentiated) first. We discovered a specific growth factor (hepatocyte growth factor, HGF) in rat platelets. Exceptionally, I also worked on branched chain amino acids (valine, leucine and isoleucine). These amino acids are not efficiently metabolized in the liver, so I had to consider the physiology of extrahepatic tissues as well. Finally, I came across a huge protease complex, the proteasome. Whether these players, small amino acid metabolizing enzymes and the huge protease complex, danced well in harmony on my playground or not, I still do not know.     

聚甲基丙烯酸甲酯-丙烯酸酰胺嵌段共聚物的合成与表征

引发剂;苯胺;聚甲基丙烯酸甲酯-丙烯酸酰胺嵌段共聚物的合成与表征     

Improved Protocol for Thorpe Reaction: Synthesis of 4‐Amino‐1‐arylpyrazole using Solid–Liquid Phase‐Transfer Conditions

Solid–liquid phase‐transfer conditions were employed for the first time in the Thorpe reaction to synthesize 4‐amino‐1‐aryl‐3,5‐substituted‐1H‐pyrazoles 3. Aryl amines were diazotized and coupled with various active methylene compounds such as cyano acetamide, cyanoacetophenone, malononitrile, and ethyl cyanoacetate, resulting into α‐arylhydrazononitriles 1. Cyclization of 1 using α‐bromo ketones or esters resulted in compounds 3.     

Organocatalytic Conjugate Addition of Azide Ion to α,β‐Unsaturated Aldehydes

An efficient and simple amine‐catatalyzed azide conjugate addition to α,β‐unsaturated aldehydes has been developed. In the presence of a catalytic amount of tertiary amine with a 1:1 mixture of NaN₃ and 37% HCl in CH₂Cl₂, α,β‐unsaturated aldehydes provided β‐azido aldehydes, which could be transformed into 1,3‐amino alcohols.     

Catalytic Asymmetric Construction of Quaternary α‐Amino Acid Containing Pyrrolidines through 1,3‐Dipolar Cycloaddition of Azomethine Ylides to α‐Aminoacrylates

The first catalytic enantioselective 1,3‐dipolar cycloaddition of azomethine ylides to α‐aminoacrylate catalyzed by a AgOAc/ferrocenyl oxazolinylphosphine (FOXAP) system was developed, which exhibits excellent exo‐ and enantioselectivity (92–99 % ee). This process provides efficient access to useful 4‐aminopyrrolidine‐2,4‐dicarboxylic acid (APDC)‐like compounds containing a unique quaternary α‐amino acid unit.