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）.

Artificial Fish Swarm for Multi Protein Sequences Alignment in Bioinformatics

The alignment operation between many protein sequences or DNAsequences related to the scientific bioinformatics application is very complex.There is a trade-off in the objectives in the existing techniques of MultipleSequence Alignment (MSA). The techniques that concern with speed ignoreaccuracy, whereas techniques that concern with accuracy ignore speed. Theterm alignment means to get the similarity in different sequences with highaccuracy. The more growing number of sequences leads to a very complexand complicated problem. Because of the emergence;rapid development;anddependence on gene sequencing, sequence alignment has become importantin every biological relationship analysis process. Calculating the numberof similar amino acids is the primary method for proving that there is arelationship between two sequences. The time is a main issue in any alignmenttechnique. In this paper, a more effective MSA method for handling themassive multiple protein sequences alignment maintaining the highest accuracy with less time consumption is proposed. The proposed method dependson Artificial Fish Swarm (AFS) algorithm that can break down the mostchallenges of MSA problems. The AFS is exploited to obtain high accuracyin adequate time. ASF has been increasing popularly in various applicationssuch as artificial intelligence, computer vision, machine learning, and dataintensive application. It basically mimics the behavior of fish trying to getthe food in nature. The proposed mechanisms of AFS that is like preying,swarming, following, moving, and leaping help in increasing the accuracy andconcerning the speed by decreasing execution time. The sense organs that aidthe artificial fishes to collect information and vision from the environmenthelp in concerning the accuracy. These features of the proposed AFS make thealignment operation more efficient and are suitable especially for large-scaledata. The implementation and experimental results put the proposed AFS as afirst choice in the queue of alignment compared to the well-known algorithmsin multiple sequence alignment.

Chaos game representation walk model for the protein sequences

A new chaos game representation of protein sequences based on the detailed hydrophobic-hydrophilic （HP） model has been proposed by Yu et al （Physica A 337（2004） 171）. A CGR-walk model is proposed based on the new CGR coordinates for the protein sequences from complete genomes in the present paper. The new CCR coordinates based on the detailed HP model are converted into a time series, and a long-memory ARFIMA（p, d, q） model is introduced into the protein sequence analysis. This model is applied to simulating real CCR-walk sequence data of twelve protein sequences. Remarkably long-range correlations are uncovered in the data and the results obtained from these models are reasonably consistent with those available from the ARFIMA（p, d, q） model.

Analysis on n-gram statistics and linguistic features of whole genome protein sequences

To obtain the statistical sequence analysis on a large number of genomic and proteomic sequences available for different organisms, the n-grams of whole genome protein sequences from 20 organisms were extracted. Their linguistic features were analyzed by two tests: Zipf power law and Shannon entropy, developed for analysis of natural languages and symbolic sequences. The natural genome proteins and the artificial genome proteins were compared with each other and some statistical features of n-grams were discovered. The results show that: the n-grams of whole genome protein sequences approximately follow the Zipf law when n is larger than 4; the Shannon n-gram entropy of natural genome proteins is lower than that of artificial proteins; a simple uni-gram model can distinguish different organisms; there exist organism-specific usages of "phrases" in protein sequences. It is suggested that further detailed analysis on n-gram of whole genome protein sequences will result in a powerful model for mapping the relationship of protein sequence, structure and function.

Proteins:From sequence to structure

Protein sequences as special heterogeneous sequences are rare in the amino acid sequence space. The specific sequen- tial order of amino acids of a protein is essential to its 3D structure. On the whole, the correlation between sequence and structure of a protein is not so strong. How well would a protein sequence contain its structural information？ How does a sequence determine its native structure？ Keeping the globular proteins in mind, we discuss several problems from sequence to structure.

Antibody-Like Phosphorylation Sites in Focus of Statistically Based Bilingual Approach

In accordance with previous reports, the sequences related to phosporylated protein segments occur in conserved variable domains of immunoglobulins including first of all certain N-terminally located segments. Consequently, we look here for the sequences 1) composing human and mouse proteins different from antigen receptors, 2) identical with or highly similar to nucleotide sequence representatives of conserved variable immunoglobulin segments and 3) identical with or closely related to phosphorylation sites. More precisely, we searched for the corresponding actual pairs of DNA and protein sequence segments using five-step bilingual approach employing among others a) different types of BLAST searches, b) two in-principle-different machine-learning methods predicting phosphorylated sites and c) two large databases recording existing phosphorylation sites. The approach identified seven existing phosphorylation sites and thirty-seven related human and mouse segments achieving limits for several predictions or phylogenic parameters. Mostly serines phosporylated with ataxia-telangiectasia-related kinase (involved in regulation of DNA-double-strand-break repair) were indicated or predicted in this study. Hypermutation motifs, located in effective positions of the selected sequence segments, occurred significantly less frequently in transcribed than non-transcribed DNA strands suggesting thus the incidence of mutation events. In addition, marked differences between the numbers and proportions of human and mouse cancer-related sequence items were found in different steps of selection process. The possible role of hypermutation changes within the selected segments and the observed structural relationships are discussed here with respect to DNA damage, carcinogenesis, cancer vaccination, ageing and evolution. Taken together, our data represent additional and sometimes perhaps complementary information to the existing databases of empirically proven phosphorylation sites or pathogenically important spots.

SATB2-associated syndrome caused by a novel SATB2 mutation in a Chinese boy:A case report and literature review

BACKGROUND Special AT-rich sequence binding protein 2(SATB2)-associated syndrome(SAS;OMIM 612313)is an autosomal dominant disorder.Alterations in the SATB2 gene have been identified as causative.CASE SUMMARY We report a case of a 13-year-old Chinese boy with lifelong global developmental delay,speech and language delay,and intellectual disabilities.He had short stature and irregular dentition,but no other abnormal clinical findings.A de novo heterozygous nonsense point mutation was detected by genetic analysis in exon 6 of SATB2,c.687C>A(p.Y229X)(NCBI reference sequence:NM_001172509.2),and neither of his parents had the mutation.This mutation is the first reported and was evaluated as pathogenic according to the guidelines from the American College of Medical Genetics and Genomics.SAS was diagnosed,and special education performed.Our report of a SAS case in China caused by a SATB2 mutation expanded the genotype options for the disease.The heterogeneous manifestations can be induced by complicated pathogenic involvements and functions of SATB2 from reviewed literatures:(1)SATB2 haploinsufficiency;(2)the interference of truncated SATB2 protein to wild-type SATB2;and(3)different numerous genes regulated by SATB2 in brain and skeletal development in different developmental stages.CONCLUSION Global developmental delays are usually the initial presentations,and the diagnosis was challenging before other presentations occurred.Regular follow-up and genetic analysis can help to diagnose SAS early.Verification for genes affected by SATB2 mutations for heterogeneous manifestations may help to clarify the possible pathogenesis of SAS in the future.

Recombinant scorpion insectotoxin AaIT kills specifically insect cells but not human cells

The nucleotide sequence deduced from the amino acid sequence of the scorpion insectotoxin AaIT was chemically synthesized and was expressed in Escherichia coli. The authenticity of this in vitro expressed peptide was confirmed by N-terminal peptide sequencing. Two groups of bioassays, artificial diet incorporation assay and contact insecticidal effect assay, were carried out separately to verify the toxicity of this recombinant toxin. At the end of a 24 h experimental period, more than 60% of the testing diamondback moth (Plutella xylostella) larvae were killed in both groups with LC50 value of 18.4 microM and 0.70 microM respectively. Cytotoxicity assay using cultured Sf9 insect cells and MCF-7 human cells demonstrated that the toxin AaIT had specific toxicity against insect cells but not human cells. Only 0.13 microM recombinant toxin was needed to kill 50% of cultured insect cells while as much as 1.3 microM toxin had absolutely no effect on human cells. Insect cells produced obvious intrusions from their plasma membrane before broken up. We infer that toxin AaIT bind to a putative sodium channel in these insect cells and open the channel persistently, which would result in Na+ influx and finally cause destruction of insect cells.

Machine intelligence,rough sets and rough-fuzzy granular computing:uncertainty handling in bio-informatics and Web intelligence

Machine intelligence,is out of the system by the artificial intelligence shown.It is usually achieved by the average computer intelligence.Rough sets and Information Granules in uncertainty management and soft computing and granular computing is widely used in many fields,such as in protein sequence analysis and biobasis determination,TSM and Web service classification Etc.

The effect of baicalein on the expression of SATB1 in MDA-MB-231 cells

Baicalein had been proved to have anti-cancer activity in vitro and in vivo, including the inhibition of malignant proliferation, migration, adhesion and invasion of many kinds of cancer cells. The special AT-rich sequence binding protein 1 （SATB1） is a tissue-specific expression of nuclear matrix-binding protein and is reported to be a breast cancer ＂gene group organizer＂. Previous studies have shown that SATB1 is involved in the growth, metastasis and prognosis of breast cancer. The present study was aimed to investigate whether baicalein inhibits the proliferation and migration of MDA-MB-231 human breast cancer cells through down-regulation of the SATB1 expression. Methods： MDA-MB-231 cells were treated for 24 h, 48 h and 72 h with various concentrations of baicalein （0, 5, 10, 20, 40 and 80 pM） respectively. Then, the proliferation and migration of MDA-MB-231 cells following treatment with baicalein were determined using colorimetric 3-（4, 5-dimethylthia- zol-2-yl） 2, 5-diphenyltetrazolium bromide （MTT） and wound healing assays. Thereafter, western blot analysis was performed to detect the changes of SATB1 protein expression in MDA-MB-231 cells. Results： Along with the prolongation of time and increase of drug concentration, inhibitory effect of baicalein on proliferation and migration of MDA-MB-231 cells gradually in- creased, in a time.- and dose- dependent manner （P 〈 0.05）. Meanwhile, after treated with baicalein in different concentrations for 48 h, the level of SATB1 protein expression of MDA-MB-231 cells decreased obviously, in a dose-dependent manner （P 〈 0.05）. Conclusion： Baicalein inhibits breast cancer cell proliferation and suppresses its invasion and metastasis by reducing cell migration possibly by down-regulation of the SATB1 protein expression, indicating that baicalein is a potential therapeutic agent for human breast cancer.

Nontuberculous Mycobacteria Infections in Katavi Rukwa Ecosystems

A study on nontuberculous mycobacteria （NTM） was carried out in wildlife-livestock interface of Katavi Rukwa ecosystem （KRE）. 328 livestock tissues and 178 wild animals were cultured, wild animals were sampled opportunistically during professional hunting and game cropping operations in the KRE protected areas. The objective of the study was to generate data on epidemiology of NTM in the wildlife-livestock interface of the KRE. Methods used to identify the NTM were： culture and isolation, polymerase chain reaction, protein heat shock 65 kilodalton （hsp65） and sequencing. Mycobacteria were detected on 25.9% and 11.9% of livestock and wildlife tissue cultures, respectively. The most NTM isolated were M. kansasii （30%）, M. gastri （30%）, M. fortuitum （1%）, M. intracellulare （4%）, M. indicuspranii （4%）, M. nonchromogenicum （6%） and M. lentiflavum （6%）. Other NTM in smaller percentages were M. hibernae, M. engbaekii, M. septicum, M. arupense and 34.. godii. Due to rise of NTM infection in both human and animals, it is recommended that awareness and laboratory facilities be improved to curb the underreporting especially in TB-endemic countries. For species specific identification, a network of national and regional laboratories is promoted.

Rationally designed synthetic peptide as versatile calibrant to improve the accuracy of protein sequence analysis using MALDI mass spectrometry

Matrix-assisted laser desorption/ionization(MALDI)mass spectrometry(MS)plays an indispensable role in analyzing protein covalent structures.The reliable identification of amino acid residues and modifications relies on the mass accuracy,which is highly dependent on calibration.However,the accuracy provided by the currently available calibrants still needs further improvement in terms of compatibility with multiple tandem MS modes or ion polarity modes,calibratable range,and minimizing suppression of and interference with analyte signals.Here aiming at developing a versatile calibrant to solve these problem,we designed a synthetic peptide format of calibrant R_x(GDP_n)_m(referred to as“Gly-Asp-Pro,GDP”)according to the chemical natures of amino acids and polypeptide fragmentation rules in tandem MS.With four types of amino acid residues selected and arranged through rational designs,a GDP peptide produces highly regulated fragments that give rise to evenly spaced signals in each tandem MS mode and is compatible with both positive and negative ion modes.In internal calibration,its regulated fragmentation pattern minimizes interference with analyte signals,and using a single peptide as the input minimizes suppression of the analyte signals.As demonstrated by analyses of proteins including monoclonal antibody and Aβ-42,these features allowed significant increase of the mass accuracy and precision,which improved sequence coverage and sequence resolution in sequence analyses(including de novo sequencing).This rational design strategy may also inspire further development of synthetic calibrants that benefit structural analysis of biomolecules.

Overexpression of a novel gene , Cms1, can rescue the growth arrest of a Saccharomyces cerevisiae mcm10 suppressor

MCM10 protein is an essential replication factor involved in the initiation of DNA replication. A mcm10 mutant (mcm10-1) of budding yeast shows a growth arrest at 37 degrees C. In the present work, we have isolated a mcm10-1 suppressor strain, which grows at 37 degrees C. Interestingly, this mcm10-1 suppressor undergoes cell cycle arrest at 14 degrees C. A novel gene, YLR003c, is identified by high-copy complementation of this suppressor. We called it as Cms1 (Complementation of Mcm 10 Suppressor). Furthermore, the experiments of transformation show that cells of mcm10-1 suppressor with high-copy plasmid but not low-copy plasmid grow at 14 degrees C, indicating that overexpression of Cms1 can rescue the growth arrest of this mcm10 suppressor at non-permissive temperature. These results suggest that CMS1 protein may functionally interact with MCM10 protein and play a role in the regulation of DNA replication and cell cycle control.

Targeted protein editing technique in living mammalian cells by peptide-fused PNGase

Various precise gene editing techniques at the DNA/RNA level,driven by clustered regularly interspaced short palindrome repeats(CRISPR)/CRISPR-associated protein 9(Cas9)technology,have gained significant prominence.Yet,research on targeted protein editing techniques remains limited.Only a few attempts have been made,including the use of specific proteases and de-O-glycosylating enzymes as editing enzymes.Here,we propose direct editing of Nglycosylated proteins using de-N-glycosylating enzymes to modify N-glycosylation and simultaneously alter the relevant asparagine residue to aspartate in living cells.Selective protein deglycosylation editors were developed by fusing high-affinity protein-targeting peptides with active peptide:N-glycanases(PNGases).Three crucial cell membrane proteins,programmed cell death protein-1(PD-1),programmed cell death-1 ligand 1(PD-L1),and severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)spike protein,were chosen to be tested as a proof of concept.N-linked glycans were removed,and the relevant sites were converted from Asn to Asp in living mammalian cells,destabilizing target proteins and accelerating their degradation.Further investigation focused on SARS-CoV-2 spike protein deglycosylation editing.The collaboration of LCB1-PNGase F(PNGF)effectively reduced syncytia formation,inhibited pseudovirus packaging,and significantly hindered virus entry into host cells,which provides insights for coronavirus disease 2019(COVID-19)treatment.This tool enables editing protein sequences post-de-N-glycosylation in living human cells,shedding light on protein N-glycosylation functions,and Asn to Asp editing in organisms.It also offers the potential for developing protein degradation technologies.

MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction

Mitotic catastrophe(MC)is a form of programmed cell death induced by mitotic process disorders,which is very important in tumor prevention,development,and drug resistance.Because rapidly increased data for MC is vigorously promoting the tumor-related biomedical and clinical study,it is urgent for us to develop a professional and comprehensive database to curate MC-related data.Mitotic Catastrophe Database(MCDB)consists of 1214 genes/proteins and 5014 compounds collected and organized from more than 8000 research articles.Also,MCDB defines the confidence level,classification criteria,and uniform naming rules for MC-related data,which greatly improves data reliability and retrieval convenience.Moreover,MCDB develops protein sequence alignment and target prediction functions.The former can be used to predict new potential MC-related genes and proteins,and the latter can facilitate the identification of potential target proteins of unknown MC-related compounds.In short,MCDB is such a proprietary,standard,and comprehensive database for MC-relate data that will facilitate the exploration of MC from chemists to biologists in the fields of medicinal chemistry,molecular biology,bioinformatics,oncology and so on.The MCDB is distributed on http://www.combio-lezhang.online/MCDB/indexhtml/.

A mirror-image protein-based information barcoding and storage technology

A mirror-image protein-based information barcoding and storage technology wherein D-amino acids are used to encode information into mirror-image proteins that are chemically synthesized is described.These mirror-image proteins were then fused into various materials from which information-encoded objects were produced.Subsequently,the mirror-image proteins were extracted from the objects using biotin-streptavidin resin-mediated specific enrichment and cleaved using an Ni(Ⅱ)-mediated selective peptide cleavage.Protein sequencing was accomplished using liquid chromatography/tandem mass spectrometry(LC-MS/MS)and then transcoded into the recorded information.We demonstrated the use of this technology to encode Chinese words into mirror-image proteins,which were then fused onto a poly(ethylene terephthalate)(PET)film and retrieved and decoded by LC-MS/MS sequencing.Compared to information barcoding and storage technologies using natural biopolymers,the mirrorimage biopolymers used in our technology may be more stable and durable.

Expressions of farnesoid X receptor and myeloid cell leukemia sequence 1 protein are associated with poor prognosis in patients with gallbladder cancer

Background Farnesoid X receptor （FXR） regulates tumorigenesis, but its clinical significance in gallbladder cancer （GBC） remains unclear. This study investigated its clinical and prognostic significance in GBC patients, as well as its association with the anti-apoptotic protein, myeloid cell leukemia sequence 1 （MCL1） protein. Methods FXR and MCL1 expression in 42 primary GBC and 15 normal gallbladder tissues were analyzed by immunohistochemistry. The patients and samples were collected from Ren Ji Hospital from January 2005 to December 2010. Their association with clinicopathologic factors and prognosis, as well as the correlation between FXR and MCL1 protein expression were analyzed by statistical analyses. Results Compared with normal gallbladder tissues, FXR expression was decreased and MCL1 expression was increased in GBC, during progression of tumor node metastasis （TNM） stage. The Kaplan-Meier survival analysis showed that FXR low-expression and MCL1 over-expression were significantly associated with overall poor survival. Furthermore, multivariate analysis showed that FXR and MCL1 are both prognostic factors for GBC patients. FXR low-expression was significantly correlated with MCL1 over-expression. Conclusion FXR might be a new molecular marker to predict the prognosis of patients with GBC and a novel therapeutic target. Chin Med J 2014;127 （14）： 2637-2642

Adaptive nanopores:A bioinspired label-free approach for protein sequencing and identification

Single molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches.However,its technological realization can only be envisioned,and huge challenges need to be overcome.Major difficulties are inherent to the structure of proteins,which are composed by several different amino-acids.Despite long standing efforts,only few complex techniques,such as Edman degradation,liquid chromatography and mass spectroscopy,make protein sequencing possible.Unfortunately,these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement.It is known that proteins can distinguish closely similar molecules.Moreover,several proteins can work as biological nanopores in order to perform single molecule detection and sequencing.Unfortunately,while DNA sequencing by means of nanopores is demonstrated,very few examples of nanopores able to perform reliable protein-sequencing have been reported sofar.Here,we investigate,by means of molecular dynamics simulations,how a re-engineered protein,acting as biological nanopore,can be used to recognize the sequence of a translocating peptide by sensing the MshapeH of individual amino-acids.In our simulations we demonstrate that it is possible to discriminate with high fidelity,9 different amino-acids in a short peptide translocating through the engineered construct.The method,here shown for fluorescence-based sequencing,does not require any labelling of the peptidic analyte.These results can pave the way for a new and highly sensitive method of sequencing.

Protein sequence analysis based on hydropathy profile of amino acids

Biology sequence comparison is a fundamental task in computational biology.According to the hydropathy profile of amino acids,a protein sequence is taken as a string with three letters.Three curves of the new protein sequence were defined to describe the protein sequence.A new method to analyze the similarity/dissimilarity of protein sequence was proposed based on the conditional probability of the protein sequence.Finally,the protein sequences of ND6(NADH dehydrogenase subunit 6)protein of eight species were taken as an example to illustrate the new approach.The results demonstrated that the method is convenient and efficient.

Cloning and characterization of cholesteryl ester transfer protein isolated from the tree shrew

Objective To obtain the nucleotide sequence and deduced amino acid sequence of cholesteryl ester transfer protein (CETP) cDNA from the tree shrew (Tupaia glis).Methods The cDNA sequence of the tree shrew CETP was obtained by utilizing the technique of switching mechanism at 5' end of RNA transcript (SMART) and rapid amplification of cDNA end (RACE) from the first strand of the cDNA. The amino acid sequence of CETP was deduced from the cDNA sequence and its primary and secondary structures were predicted.Results The sequence of CETP cDNA from tree shrew (GenBank accession number AF334033) covers 1636 bp, including 178 bp at the 3' end of the untranslated region and a 1458 bp fragment in a coding region, which provides the complete sequence of mature tree shrew CETP, although not the initiator methionine. The first 24 bp encodes a partial signal peptide. The mature protein consists of 477 amino acids and is longer than the human version by one amino acid (Gly318). Comparing this amino acid sequence with those of other animals' CETPs, the identity between tree shrew and human and rabbit CETP is 88% and 82%, respectively. The protein is extremely hydrophobic as it contains many hydrophobic residues, especially at the C-terminal, consistent with its function in the transfer of neutral lipids. The amino acid residues concerning with binding and transferring neutral lipids are highly conserved. There is a deletion of an N-linked glycosylation site at Asn342 in the tree shrew CETP protein that may participate in the removal of peripheral cholesterol and cholesteryl ester by increasing its activity of transferring cholesteryl ester.Conclusion The possible glycosylation in the tree shrew CETP may be involved in the molecular mechanism of its insusceptibility to atherosclerosis.