Prediction of Side Chain Orientations in Proteins by Statistical Machine Learning Methods

Abstract

We develop ways to predict the side chain orientations of residues within a protein structure by using several different statistical machine learning methods. Here side chain orientation of a given residue i is measured by an angle Ω_i between the vector pointing from the center of the protein structure to the C^α _i atom and the vector pointing from the C^α _i atom to the center of its side chain atoms. To predict the Ω_i angles, we construct statistical models by using several different methods such as general linear regression, a regression tree and bagging, a neural network, and a support vector machine. The root mean square errors for the different models range only from 36.67 to 37.60 degrees and the correlation coefficients are all between 30% and 34%. The performances of different models in the test set are, thus, quite similar, and show the relative predictive power of these models to be significant in comparison with random side chain orientations.     

Solid support-dependent alkylation of tryptophan residues in SPPS using a 2-methoxybenzyl alcohol-based linker

Summary Several side reactions can be encountered in the synthesis of Trp-containing peptides, due to molecular species originating from side chain-protecting groups or from the linker during acidolytic cleavage of the peptide from the resin. The linker can be the source of both alkylation in solution of the indole moiety of the tryptophan side chain and permanent readdition of the cleaved peptide to the resin. We report that both these reactions occur at a high level during the synthesis of Trp-containing peptides on a PEG-PS resin containing a 2-methoxybenzyl alcohol-based linker, in spite of the presence of suitable scavengers in the TFA-based cleavage mixture. Both side reactions are efficiently prevented by the use of a protected analogue of tryptophan, namely N^im-Boc-Trp, previously reported for the synthesis of peptides containing tryptophan and arginine residues.     

自动三维度量学及在人体头面部测量中的应用

本文叙述一种新的无需参考物体或平面的自动三维度量学测量系统的原理,以及应用这种系统对人体头面部进行测量。     

Analysis of Relationship Between Genetic Diversity and Taxol Content of Taxus wallichiana var. wallichiana in Different Provenance

We studied the relationship between genetic diversity and taxol content of Taxus wallichiana var. wallichiana using AFLP and HPLC . The results of AFLP fingerprinting indicated that two patterns were discovered among seven populations. Through PopGene 1 . 31 and Arlequin 3. 1 software , stable genetics within population and significant differentiation among populations (F_st = 0. 67 ) were revealed . However, taxol content was markedly different within and among populations when testing the one-year twigs . Among wild forests, the highest taxol content was found in Luxi population which average percentage was 0. 0185%. While the taxol content level was low in Tengchong and Yongde populations , which were 0. 0049% and 0. 0087% respectively . The cultivated population in Lufeng showed the highest taxol content level which was 0. 0225% comparing with that in the populations of wild forests. There were relations between genetic diversity and taxolcontent at the population level to some extent , while no corresponding relations were found at the individual level .     

Mapping and Analysis of a Yellow Mutant chlm-4 of Arabidopsis thaliana (Cruciferae)

Chlorophylls are essential for photosynthesis. Chlorophyll biosynthesis is catalyzed by a series of enzyme complexes, such as Mg protoporphyrin IX methyltransferase. A yellow mutant of Arabidopsis was isolated using an enthyl methane sulfonate (EMS) mutagenesis strategy. Chlorophyll content dramatically reduced and grana stacking was absent in the mutant. Genetic analysis indicated that the mutant was controlled by a single recessive gene. Using map based cloning strategy, the gene responsible for the mutant phenotype was mapped to a region of 114 kb between the molecular markers F13M23 and T30C3 on chromosome 4, in which the CHLM gene encoding Mg protoporphyrin IX methyltransferase was included. The mutant was proved to be an allelic mutant of CHLM gene by sequencing and allelism test and then was designated as chlm 4. Gly59 of CHLM was replaced by Glu59 in chlm 4, which indicated that Gly59 was essential for the function of Mg protoporphyrin IX methyltransferase.