The structural analysis of protein sequences based on the quasi-amino acids code

Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Cenome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system （∑, ＋, ＊） is introduced, where ∑ is the set of 64 codons. According to the characteristics of （∑, ＋, ＊）, a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al （2003 J. Anhui Agricultural University 30 439）, the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that （ZU, ＋,×） is a field. Furthermore, the operational results display that the eodon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al （2002 Acta Biophysiea Siniea 18（1） 87）. The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of ＇the 64 codon assignments of mRNA to amino acids is probably completely wrong＇ proposed by Yang （2006 Progress in Modern Biomedicine 6 3）.

A reduced computational load protein coding predictor using equivalent amino acid sequence of DNA string with period-3 based time and frequency domain analysis

Development of efficient gene prediction algorithms is one of the fundamental efforts in gene prediction study in the area of genomics. In genomic signal processing the basic step of the identification of protein coding regions in DNA sequences is based on the period-3 property exhibited by nucleotides in exons. Several approaches based on signal processing tools and numerical representations have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new indicator sequence based on amino acid sequence, called as aminoacid indicator sequence, derived from DNA string that uses the existing signal processing based time-domain and frequency domain methods to predict these regions within the billions long DNA sequence of eukaryotic cells which reduces the computational load by one-third. It is known that each triplet of bases, called as codon, instructs the cell machinery to synthesize an amino acid. The codon sequence therefore uniquely identifies an amino acid sequence which defines a protein. Thus the protein coding region is attributed by the codons in amino acid sequence. This property is used for detection of period-3 regions using amino acid sequence. Physico-chemical properties of amino acids are used for numerical representation. Various accuracy measures such as exonic peaks, discriminating factor, sensitivity, specificity, miss rate, wrong rate and approximate correlation are used to demonstrate the efficacy of the proposed predictor. The proposed method is validated on various organisms using the standard data-set HMR195, Burset and Guigo and KEGG. The simulation result shows that the proposed method is an effective approach for protein coding prediction.

Pathogenicity and amino acid sequences of hemagglutinin cleavage site and neuraminidase stalk of differently passaged H9N2-avian influenza virus in broilers

Low pathogenic Avian Influenza (AI) virus has the ability to evolve to high pathogenic viruses resulting in significant economic losses in the poultry sector. This study aims at assessing the impact of H9N2 viral passaging in broilers and its relatedness to pathogenicity and amino acid (a.a) sequences of the hemagglutinin (HA) cleavage site and neuraminidase (NA) stalk. The original H9N2 AI virus (P0) was used to challenge ten-21 days old broilers. Individual recovery of H9N2 virus from homogenates of trachea, lungs and airsacs was attempted in 9 days old chicken embryos, as a conclusion of the first passage (P1). Tracheal isolates of H9N2 were passaged for a second (P2) and a third (P3) time in broilers, followed by a similar embryonic recovery procedure. The a.a. sequence of a part of HA1 cleavage site and Neuraminidase stalk were compared among the differently passaged viruses;an assessement of the relatedness of the determined a.a. sequences to the pathogenicity in broilers, based on frequency of mortality, morbidity signs, gross and microscopic lesions at 3 days post challenge with the P1, P2, and P3-H9N2, is concluded. An increase in certain morbidity signs and specific lesions was observed in P2- and P3-H9N2 challenged broilers compared to birds challenged with P1-H9N2. A conserved R-S-S-R amino acid sequence at the HA1 cleavage site was observed in the differently passaged H9N2, associated with a variability in the NA stalk-a.a sequences. The passaging of the low pathogenic H9N2 virus in broilers leads to a trend of increase in pathogenicity, manifested in higher frequency of morbidity signs, and of specific gross and microscopic lesions of the examined organs. This passaging was associated with a conserved a.a. sequence of the hemaglutinin cleavage site and a variability in the sequence of the neuraminidase stalk. A detailed study of the potential of the detected variability in the neuraminidase stalk of H9N2 in induction of a higher pathogenicity in broilers will be the subject of future investigations.

Using Chou’s Pseudo Amino Acid Composition for Protein Remote Homology Detection

Protein remote homology detection is a key problem in bioinformatics. Currently, the discriminative methods, such as Support Vector Machine (SVM), can achieve the best performance. The most efficient approach to improve the performance of the SVM-based methods is to find a general protein representation method that is able to convert proteins with different lengths into fixed length vectors and captures the different properties of the proteins for the discrimination. The bottleneck of designing the protein representation method is that native proteins have different lengths. Motivated by the success of the pseudo amino acid composition (PseAAC) proposed by Chou, we applied this approach for protein remote homology detection. Some new indices derived from the amino acid index (AAIndex) database are incorporated into the PseAAC to improve the generalization ability of this method. Our experiments on a well-known benchmark show this method achieves superior or comparable performance with current state-of-the-art methods.

Sequence Pattern Correlation of Amino Acid in Collision-induced Dissociation Electrospray Ionization Mass Spectrometry

A novel approach of sequence pattern correlation has been applied to predict an expected amino acid sequence from CID ESI MS spectra. The proposed approach deduces sequence patterns with no help from known protein database such that it is useful to identify an unknown peptide or new protein. The algorithm applies a cross correlation to match an experimental CID spectrum with predicted sequence pattern generated from fragmentation information. The fragmentation knowledge of both y series and other non y series are utilized to generate the predicted sequence patterns. In contrast to the normal de novo approach, the proposed approach is insensitive to mass tolerance and non susceptive to spectral integrality with no need for selection of a starting point.

Amino Acid Sequence of an Excitatory Insect-selective Toxin (BmK IT) From Venom of the Scorpion Buthus martensi Karsch

The insect-selective neurotoxin(BmK IT) of scorpion Buthus martensi Karsch was first reduced and S-alkylated, and then digested by TPCK-trypsin and Staphylococcus aureus V-8 Protease. The enzymatic peptides were purified on TLC-plastic sheet and submitted to determine their amino acid compositions and sequences. The sequence of the 70 amino acid residues of BmK IT was established with reference to the primary structure of AaH IT, another excitatory insect-selective toxin from the venom of North African scorpion Androctonus australis Hector. About 75% of the homologous sequence was found in the molecules of BmK IT and AaH IT. It is obvious that the results contribute toward better understanding of the molecular structure characteristics, structure/activity relationship of scorpion insect-selective toxins, and they can serve as the molecular basis for utilizing the toxins as a tool to clarify molecular mechanism involved in channel gating, and to infer the possibility of developing them as new selective bioinsecticides.

The Variability of Amino Acid Sequences in Hepatitis B Virus

Hepatitis B virus(HBV) is an important human pathogen belonging to the Hepadnaviridae family, Orthohepadnavirus genus. Over 240 million people are infected with HBV worldwide. The reverse transcription during its genome replication leads to low fidelity DNA synthesis, which is the source of variability in the viral proteins. To investigate the variability quantitatively, we retrieved amino acid sequences of 5,167 records of all available HBV genotypes(A–J) from the Genbank database. The amino acid sequences encoded by the open reading frames(ORF) S/C/P/X in the HBV genome were extracted and subjected to alignment. We analyzed the variability of the lengths and the sequences of proteins as well as the frequencies of amino acids. It comprehensively characterized the variability and conservation of HBV proteins at the level of amino acids. Especially for the structural proteins, hepatitis B surface antigens(HBsAg), there are potential sites critical for virus assembly and immune recognition. Interestingly, the preS1 domains in HBsAg were variable at some positions of amino acid residues, which provides a potential mechanism of immune-escape for HBV, while the preS2 and S domains were conserved in the lengths of protein sequences. In the S domain, the cysteine residues and the secondary structures of the alpha-helix and beta-sheet were likely critical for the stable folding of all HBsAg components. Also, the preC domain and C-terminal domain of the core protein are highly conserved. However, the polymerases(HBpol) and the HBx were highly variable at the amino acid level. Our research provides a basis for understanding the conserved and important domains of HBV viral proteins, which could be potential targets for anti-virus therapy.

Amino acid identification and sequence analysis of peptides by reaction mass spectrometry

Fast atom bombardment mass spectrometry (FAB-MS) is applied to distinguish N- terminal series ions from C-terminal series ions of a peptide by on-probe acetylation, it provides valuable information about the sequence of an unknown peptide. The FAB mass spectra contain a number of characteristic ions at low-mass region in addition to the sequence ions at high-mass region. It was found that the ions below m/z 200 are characteristic of the amino acid composition of the peptide, from which the amino acid composition of the peptide could be estimated. Additionally, mixture analysis is also discussed.

The amino acid sequence of a double-headed trypsin inhibitor from the seeds of Momordica charantia Linn.Cucurbitaceae

A double-headed trypsin inhibitor(MCI-1)was isolated and purified from the seeds of Momordica charantia Linn.Cucurbitaceae,by using the trypsin-sepharose-4B affinity chroma- tography and CM-Sephadex-C50 ion exchange chromatography.It is composed of 77 amino acid residues:Asp_8 Thr_1 Ser_4 Glu_8 Pro_2 Gly_6 Ala_4 Cys_(14) Val_2 Met_4 Ile_8 Leu_1 Phe_1 His_3 Lys_ Arg_7. The amino acid sequence of MCI-1 was determined by sequencing the cyanogen bromide,tryptic and staphylococcus aureus V8 proteolytic peptides,then aligned by overlapped sequences.The result shows that MCI-1 contains 7 pairs of disulfide bonds,its sequence showed the high homology with those of “Bowman-Birk”inhibitors.About 50% trypsin inhibitory activity still remained after MCI-1 was cleavaged with cyanogen bromide.

Amino acid sequence of BmK AS, a novel polypeptide activator of ryanodine receptor on skeletal muscle

IN ref.[1],we have described a novel activator(BmK AS)of ryanodine receptor on skeletal muscle,which was obtained from the venom of scorpion Buthus martensi Karsch.This noteprovides the complete amino acid sequence of the active polypeptide,BmK AS.The molecularweight ot the polypeptide thus determined was 7 698 u,calculated based on its sequence(to-tally 66 residues),which was coincident with the value of 7 696.26 u determined by electro-

HPLC Purification and Partial Amino Acid Sequence of an α-type Insect Neurotoxin From Venom of Scorpion Buthus martensi Karsch

Scorpion venoms contain several kinds of neurotoxins, such as antimammalian neurotoxins, anti-insect neurotoxins and others. But most of them form a family of structurally related single chain proteins of 60—70 amino acid residues and selectively interact with voltage-dependent sodium channels in different excitable cells, only a few minipeptides of 31—39 amino acid residues are proved to block potassium channels. As a kind of molecular probe, scorpion neurotoxins have been widely used for analyzing the

Association Analysis of the Amino Acid Contents in Rice

The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.

Dietary protein levels and amino acid supplementation patterns alter the composition and functions of colonic microbiota in pigs

Different dietary nitrogen(N) patterns may have different effects on gut microbiota.To investigate the effects of different crude protein(CP) levels or essential amino acids(EAA) supplementation patterns on the structure and functions of colonic microbiota,42 barrows(25±0.39 kg) were randomly assigned to 7 dietary treatments including:diet 1,a high CP diet with balanced 10 EAA;diet 2,a medium CP diet with approximately 2% decreased CP level from diet 1 and balanced 10 EAA;diets 3,4,5,6 and 7,low CP diets with 4% decreased CP level from diet 1.Specifically,diet 3 was only balanced for Lys,Met,Thr and Trp;diets 4,5 and 6 were further supplemented with IIe,Val and IIe+Val on the basis of diet 3,respectively;and diet 7 was balanced for 10 EAA.Results over a 110-d trial showed that reducing the CP level by 2% or4% dramatically decreased N intake and excretion(P <0.05) in the presence of balanced 10 EAA,which was not observed when altering the EAA supplementation patterns in low CP diet(-4%).With balanced10 EAA,2% reduction in dietary CP significantly reduced Firmicutes-to-Bacteroidetes(F:B) ratio and significantly elevated the abundance of Prevotellaceae NK3 B31(P <0.05);whereas 4% reduction evidently increased the abundances of Proteobacteria,Succinivibrio and Lachnospiraceae XPB1014(P <0.05).Among the 5 low CP diets(-4%),supplementation with Ile,or Val+Ile,or balanced 10 EAA increased F:B ratio and the abundance of Proteobacteria.In addition,the predicted functions revealed that different CP levels and EAA balanced patterns dramatically altered the mRNA expression profiles of N-metabolizing genes,the "N and energy metabolism" pathways or the metabolism of some small substances,such as amino acids(AA) and vitamins.Our findings suggested that reducing the dietary CP levels by 2% to 4% with balancing 10 EAA,or only further supplementation with Ile or Val+Ile to a low protein diet(-4%) reduced the N contents entering the hindgut to various degrees,altered the abundances of N-metabolizing bacteria,and improved the abilities of N utilization.

Anaerobic digestion of sludge by different pretreatments:Changes of amino acids and microbial community

Many studies have investigated the effects of different pretreatments on the performance of anaerobic digestion of sludge.However,the detailed changes of dissolved organic nitrogen,particularly the release behavior of proteins and the byproducts of protein hydrolysis-amino acids,are rarely known during anaerobic digestion of sludge by different pretreatments.Here we quantified the changes of three types of proteins and 17 types of amino acids in sludge samples solubilized by ultrasonic,thermal,and acid/alkaline pretreatments and their transformation during anaerobic digestion of sludge.Tryptophan protein,aromatic protein I,aromatic protein II,and cysteine were identified as the key dissolved organic nitrogen responsible for methane production during anaerobic digestion of sludge,regardless of the different pretreatment methods.Different from the depletion of other amino acids,cysteine was resistant to degradation after an incubation period of 30 days in all sludge samples.Meanwhile,the“cysteine and methionine metabolism(K00270)”was absent in all sludge samples by identifying 6755 Kyoto Encyclopedia of Genes and Genomes assignments of genes hits.Cysteine contributed to the generation of methane and the degradation of acetic,propionic,and n-butyric acids through decreasing oxidation-reduction potential and enhancing biomass activity.This study provided an alternative strategy to enhance anaerobic digestion of sludge through in situ production of cysteine.

A novel vector of topological and structural information for amino acids and its QSAR applications for peptides and analogues

A new descriptor, called vector of topological and structural information for coded and noncoded amino acids (VTSA), was derived by principal component analysis (PCA) from a matrix of 66 topological and structural variables of 134 amino acids. The VTSA vector was then applied into two sets of peptide quantitative structure-activity relationships or quantitative sequence-activity modelings (QSARs/QSAMs). Molded by genetic partial least squares (GPLS), support vector machine (SVM), and immune neural network (INN), good results were obtained. For the datasets of 58 angiotensin converting enzyme inhibitors (ACEI) and 89 elastase substrate catalyzed kinetics (ESCK), the R 2, cross-validation R 2, and root mean square error of estimation (RMSEE) were as follows: ACEI, R cu 2 ?0.82, Q cu 2 ?0.77, E rmse?0.44 (GPLS+SVM); ESCK, R cu 2 ?0.84, Q cu 2 ?0.82, E rmse?0.20 (GPLS+INN), respectively.

A NEW DESCRIPA NEW DESCRIPTOR OF AMINO ACIDS BASED ON THE THREEDIMENSIONAL VECTOR OF ATOMIC INTERACTION FIELD

A noval molecular structural expression method, three-dimensional vector of atomic interac- tion field (3D-VAIF), has been newly developed based on electrostatic and steric interaction between different types of atoms. Feature descriptors of single amino acid, i.e. principal component scores of struc- tural information for amino acids (SSIA), are obtained through calculation of structural information of 20 coded amino acids using principal component analy- sis (PCA) method, and the strict tests are performed on the property of SSIA by three quantitative struc- ture-activity relationships (QSARs)/quantitative se- quence-activity models (QSAMs) models of 58 ngio- tensin-converting enzymes (ACE), 48 bitter tasting thresholds (BTT) and 31 bradykinin potentiating pentapeptides (BPP). Cumulative multiple correlation coefficients (Rc2um) are 0.789, 0.856 and 0.838; and corresponding cross-validated correlation coefficients (QL2OO) are 0.773, 0.837 and 0.815, respectively. Good results indicate that SSIA are better than tradi- tional descriptors of amino acid in quantitative se- quence-activity relationships of peptide analogues.

Rearrangement mechanism of the sodium adducts of Fmoc protected amino acids

The cationized 9-fluorenylmethoxycarbonyl (Fmoc) protected amino acids were analyzed by the electros-pray ionization tandem mass spectrometry (ESI-MS/MS). A rearrangement reaction leading to the C-terminal hydroxyl group transfer was observed. The sodium adducts of Fmoc-OH was formed. A possible rearrangement mechanism was proposed. The rearrangement reaction depended on the Fmoc group, metal ions and metal ion radius. It was shown that the Fmoc group has a strong affinity to the hydroxyl group in the gas phase.

非洲猪瘟病毒p30蛋白氨基酸序列分段表达及反应原性分析

为比较非洲猪瘟病毒(African swine fever virus,ASFV)p30蛋白氨基酸序列中不同片段的反应原性,探究p30蛋白氨基酸序列中可能的抗原优势片段。本研究通过PCR、克隆技术将p30蛋白氨基酸序列中不同片段的编码基因分别插入表达质粒pET32a,经IPTG诱导、Ni柱纯化、透析后,获得p30蛋白氨基酸序列中8~101 aa片段(P-1#)、58~101 aa片段(P-2#)、101~158 aa片段(P-3#)、8~194 aa片段(P-4#),用酶联免疫吸附试验(ELISA)分析p30蛋白氨基酸序列中不同片段与p30蛋白免疫兔血清和ASFV阳性猪血清的反应原性。结果显示,上述片段均获得诱导表达及纯化,表达形式有可溶性表达(P-1#、P-3#)和包涵体表达(P-2#、P-4#)。各片段以1.0 mg/L包被时,p30免疫兔血清与p30蛋白氨基酸序列中4种片段均能发生免疫反应,ASFV阳性猪血清与P-4#、P-1#反应较佳,与P-3#反应中等,与P-2#反应最弱。综上,p30蛋白氨基酸序列中不同片段反应原性的差异为认识p30抗原优势区域提供了数据,这将有助于非洲猪瘟血清学诊断抗原的科学筛选。

澳洲坚果抗菌肽分离纯化及其肽段鉴定与分析

以液压压榨澳洲坚果粕为原料,采用碱性蛋白酶水解制备澳洲坚果多肽(macadamia nut peptide⁃0,MNP⁃0),以对金黄色葡萄球菌与白色念珠菌的抑菌活性为跟踪指标,通过超滤、DA201⁃C型大孔吸附树脂、交联葡聚糖凝胶Sephadex G⁃25对其进行逐级分离纯化,获得抑菌活性较强的抗菌肽,并运用液相色谱串联质谱(liquid chromatography tandem mass spectrometry,LC⁃MS/MS)技术对其进行肽段组成与氨基酸序列分析。结果表明:超滤分离的不同分子量澳洲坚果多肽在所有多肽中所占质量分数不同,抑菌活性也有所差异。其中,澳洲坚果多肽组分MNP⁃4占比最高,为29.55%;抑菌活性也最强,对金黄色葡萄球菌与白色念珠菌的抑菌圈直径分别为10.01 mm与9.41 mm。大孔吸附树脂纯化多肽组分MNP⁃4的技术条件为75%乙醇溶液为解吸剂,静态吸附3 h,动态洗脱体积60 mL。经大孔吸附树脂与交联葡聚糖凝胶Sephadex G⁃25分离纯化,获得3个澳洲坚果纯化多肽(macadamia nut purified peptide,MPP)组分,其中组分MPP⁃2的抑菌活性最强,对金黄色葡萄球菌与白色念珠菌的抑菌圈直径分别为18.67 mm与16.83 mm,优于多肽MNP⁃0与超滤分离多肽组分。分离纯化的澳洲坚果抗菌活性多肽MPP⁃2含有DDLTDPAPA、VLL、WDY、VPV、WDL、LLW、LWL、FDW 8个肽段,经预测分析,属于抗菌肽的肽段为WDL与FDW,其概率得分a(1.00≥a≥0.50)均为1.00,疏水率均为66.67%,均带有1个负电荷,等电点分别为0.69与0.67,并具有较好的溶解性。研究结果表明澳洲坚果可通过酶法制备具有抗菌活性的肽类成分。

Isolation and Characterization of SARS-CoV-2 in Kenya

The discovery of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) in Wuhan, Hubei province, China, in December 2019 raised global health warnings. Quickly, in 2020, the virus crossed borders and infected individuals across the world, evolving into the COVID-19 pandemic. Notably, early signs of the virus’s existence were observed in various countries before the initial outbreak in Wuhan. As of 12th of April, the respiratory disease had infected over 762 million people worldwide, with over 6.8 million deaths recorded. This has led scientists to focus their efforts on understanding the virus to develop effective means to diagnose, treat, prevent, and control this pandemic. One of the areas of focus is the isolation of this virus, which plays a crucial role in understanding the viral dynamics in the laboratory. In this study, we report the isolation and detection of locally circulating SARS-CoV-2 in Kenya. The isolates were cultured on Vero Cercopithecus cell line (CCL-81) cells, RNA extraction was conducted from the supernatants, and reverse transcriptase-polymerase chain reaction (RT-PCR). Genome sequencing was done to profile the strains phylogenetically and identify novel and previously reported mutations. Vero CCL-81 cells were able to support the growth of SARS-CoV-2 in vitro, and mutations were detected from the two isolates sequenced (001 and 002). Genome sequencing revealed the circulation of two isolates that share a close relationship with the Benin isolate with the D614G common mutation identified along the S protein. These virus isolates will be expanded and made available to the Kenya Ministry of Health and other research institutions to advance SARS-CoV-2 research in Kenya and the region.