Biomedical subjects

Suree Phutrakul

Publications and source records attributed to Suree Phutrakul.

11 recordsLinked to original sources

PubMed2006

Enhanced detectability in proteome studies.

The discovery of candidate biomarkers from biological materials coupled with the development of detection methods holds both incredible clinical potential as well as significant challenges. However, the proteomic techniques still provide the low dynamic range of protein detection at lower abundances. This review describes the current development of potential methods to enhance the detection and quantification in proteome studies. It also includes the bioinformatics tools that are helpfully used for data mining of protein ontology. Therefore, we believe that this review provided many proteomic approaches, which would be very potent and useful for proteome studies and for further diagnostic and therapeutic applications.

Biomarkers↗

PubMed2005

Different techniques for urinary protein analysis of normal and lung cancer patients.

Many components in urine are useful in clinical diagnosis and urinary proteins are known as important components to define many diseases such as proteinuria, kidney, bladder and urinary tract diseases. In this study, we focused on the comparison of different sample preparation methods for isolating urinary proteins prior to protein analysis of pooled healthy and lung cancer patient samples. Selective method was used for preliminary investigation of some putative urinary protein markers. Urine samples were passed first through a gel filtration column (PD-10 desalting column) to remove high salts and subsequently concentrated. Remaining interferences were removed by ultrafiltration or four precipitation methods. The analysis of urinary proteins by high-performance liquid chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed many similarities in profiles among preparation methods and a few profiles were different between normal and lung cancer patients. In contrast, the results of two-dimensional gel electrophoresis (2-DE) showed more distinctly different protein patterns. Our finding showed that the sequential preparation of urinary proteins by gel filtration and ultrafiltration could retain most urinary proteins which demonstrated the highest protein spots on 2-D gels and able to identify preliminary urinary protein markers related to cancer. Although sequential preparation of urine samples by gel filtration and protein precipitation resulted in low amounts of proteins on 2-D gels, high Mr proteins were easily detected. Therefore, there are alternative choices for urine sample preparation for studying the urinary proteome and identifying urinary protein markers important for further preclinical diagnostic and therapeutic applications.

Acetone↗

PubMed2005

Functional proteomics and correlated signaling pathway of the thermophilic bacterium Bacillus stearothermophilus TLS33 under cold-shock stress.

The thermophilic bacterium Bacillus stearothermophilus TLS33 was examined under cold-shock stress by a proteomic approach to gain a better understanding of the protein synthesis and complex regulatory pathways of bacterial adaptation. After downshift in the temperature from 65 degrees C, the optimal growth temperature for this bacterium, to 37 degrees C and 25 degrees C for 2 h, we used the high-throughput techniques of proteomic analysis combining 2-DE and MS to identify 53 individual proteins including differentially expressed proteins. The bioinformatics database was used to search the biological functions of proteins and correlate these with gene homology and metabolic pathways in cell protection and adaptation. Eight cold-shock-induced proteins were shown to have markedly different protein expression: glucosyltransferase, anti-sigma B (sigma(B)) factor, Mrp protein homolog, dihydroorthase, hypothetical transcriptional regulator in FeuA-SigW intergenic region, RibT protein, phosphoadenosine phosphosulfate reductase and prespore-specific transcriptional activator RsfA. Interestingly, six of these cold-shock-induced proteins are correlated with the signal transduction pathway of bacterial sporulation. This study aims to provide a better understanding of the functional adaptation of this bacterium to environmental cold-shock stress.

Amino Acid Sequence↗

PubMed2005

Proteomics viewed on stress response of thermophilic bacterium Bacillus stearothermophilus TLS33.

Thermophilic bacterium Bacillus stearothermophilus TLS33, isolated from a hot spring in Chiang Mai, Thailand, usually produces many enzymes that are very useful for industrial applications. However, the functional properties and mechanisms of this bacterium under stress conditions are rarely reported and still need more understanding on how the bacterium can survive in stress environments. In this study, we examined the oxidative stress induced proteins of this bacterium by proteomic approach combining two-dimensional electrophoresis and mass spectrometry. When the bacterium encountered oxidative stress, peroxiredoxin, as an antioxidant enzyme, is one of the interesting stressed proteins which appeared to be systematically increased with different pI. There are four isoforms of peroxiredoxin, denoted as Prx I, Prx II, Prx III and Prx IV, which are observed at the same molecular weight of 27 kDa but differ in pI values of 5.0, 4.87, 4.81 and 4.79, respectively. The H2O2 concentration directly increased Prx II, Prx III and Prx IV intensities, but decreased Prx I intensity. These shifting of peroxiredoxin isoforms may occur by a post-translational modification. Otherwise, the longer time of oxidative stress had not affected the expression level of peroxiredoxin isoforms. Therefore, this finding of peroxiredoxin intends to know the bacterial adaptation under oxidative stress. Otherwise, this protein plays an important role in many physiological processes and able to use in the industrial applications.

Amino Acid Sequence↗

PubMed2004

Capillary electrophoresis using immobilized whole cells with overexpressed endothelin receptor for specific ligand screening.

A new capillary electrophoresis method using immobilized cells as the stationary phase has been developed. The power of this method is demonstrated by the separation and identification of endothelin antagonists on a capillary column coated by the transfected Chinese hamster ovary (CHO) cells with overexpressing endothelin receptors. The screening results are validated by functional assays suppressing the increase of intracellular calcium concentration induced by endothelin-1. Instead of making efforts in isolating protein receptors, the easily prepared whole-cell capillary column provides a superior tool on the basis of ligand/receptor affinity for a rapid screening of potent drug candidates from compound libraries.

Amino Acid Sequence↗

PubMed2003

Proteomics of snake venoms from Elapidae and Viperidae families by multidimensional chromatographic methods.

Snake venoms contain a large number of biologically active substances and the venom components are very useful for pharmaceutical applications. Our goal is to separate and identify components of snake venoms in ten snake species from the Elapidae and Viperidae families using multidimensional chromatographic methods. The multidimensional chromatographic methods include reversed-phase high-performance liquid chromatography (RP-HPLC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), lab-on-a-chip, two-dimensional electrophoresis (2-DE), and mass spectrometry. The venoms of eight snake species demonstrated major differences in hydrophobicity, molecular weight separations, and 2-DE protein distribution patterns. The 2-DE images showed major differences between families, within each family and even between the same species. Venoms of the Elapidae family showed many basic proteins with a wide range of molecular weights, while venoms of the Viperidae family showed wide ranges of pI and molecular weights, especially for Trimeresurus sp. The multidimensional chromatographic methods revealed specific differences in venom proteins intra-species as well as between species and families. We have isolated and identified proteins that may be unique for each species for further studies in the proteome of snake venoms and their potentially use in the pharmaceutical applications.

Animals↗

PubMed2002

Bioinformatics, functional genomics, and proteomics study of Bacillus sp.

The ability of bioinformatics to characterize genomic and proteomic sequences from bacteria Bacillus sp. for prediction of genes and proteins has been evaluated. Genomics coupling with proteomics, which is relied on integration of the significant advances recently achieved in two-dimensional (2-D) electrophoretic separation of proteins and mass spectrometry (MS), are now important and high throughput techniques for qualifying and analyzing gene and protein expression, discovering new gene or protein products, and understanding of gene and protein functions including post-genomic study. In addition, the bioinformatics of Bacillus sp. is embraced into many databases that will facilitate to rapidly search the information of Bacillus sp. in both genomics and proteomics. It is also possible to highlight sites for post-translational modifications based on the specific protein sequence motifs that play important roles in the structure, activity and compartmentalization of proteins. Moreover, the secreted proteins from Bacillus sp. are interesting and widely used in many applications especially biomedical applications that are the highly advantages for their potential therapeutic values.

Bacillus↗

PubMed2002

Proteomic analysis of a thermostable superoxide dismutase from Bacillus stearothermophilus TLS33.

Thermophilic bacterium Bacillus stearothermophilus TLS33 isolated from a hot spring in Chiang Mai, Thailand produces an extracellular superoxide dismutase (SOD). SOD is a free radical metabolizing enzyme that protects the cell membrane from damage by the highly reactive superoxide free radicals. To identify the secreted SOD, we used the systematically proteomic approaches of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) analysis and database searching. The bacterium was grown in a medium containing 0.1% w/v yeast extract and 0.1% w/v tryptone in 100% v/v base mixture at 65 degrees C for 72 h, by assessing their growth by protein and SOD activity. The bacterium produced the highest SOD activity at 65 degrees C for 48 h and the extracellular SOD was run on 2-D PAGE using broad range pH 3-10 immobilized pH gradients (IPGs) and narrow range pH 4-7 IPGs. The isoelectric point and molecular mass of the extracellular SOD were approximately 5.8 and 28 kDa, respectively. In addition, the NH(2)-terminal amino acid sequence was found to be P-F-E-L-P-A-L-P-Y-P-Y-D-A-L-E-P-P-I-I-D, which had a homology of approximately 85% to the Mn-SOD family and 65% to the Fe-SOD family.

Amino Acid Sequence↗

PubMed2002

Proteomic study of cold shock protein in Bacillus stearothermophilus P1: Comparison of temperature downshifts.

The thermophilic bacterium Bacillus stearothermophilus P1 is unique in its ability to thrive in extreme environments such as high temperatures or high pH conditions. The study of cold shock response is very interesting and interpreted as a shock response to express the genes involved in synthesis of specific proteins. This study investigated the study of cold shock protein of B. stearothermophilus P1 when the cell culture temperature shifted from 65 degrees C to 37 degrees C and 25 degrees C. Cell growth at 37 degrees C weakly increased in the previous 3 h and then slowly decreased. In contrast, cell growth at 25 degrees C was slowly decreased. The protein contents after temperature downshifts were analyzed by proteomic techniques using protein chip and two-dimensional (2-D) electrophoresis that are highly effective and useful for protein separation and identification. The different proteins after a temperature decrease from 65 degrees C to 37 degrees C and 25 degrees C were expressed on 2-D gel patterns and the cold shock protein was detected in the acidic area with the isoelectric point and molecular mass approximately 4.5 and 7.3 kDa, respectively. The NH(2)-terminal sequence of a major cold shock protein from B. stearothermophilus P1 was MQRGKVKWFNNEKGFGFIEVEGGSD, similar to other cold shock proteins from Bacillus sp. up to 96% identity, but different from the other bacteria with homology less than 80% identity.

Bacterial Proteins↗

PubMed2001

Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable lipase from Bacillus stearothermophilus P1.

The gene encoding a thermostable lipase secreted by Bacillus stearothermophilus P1 has been cloned and overexpressed in Escherichia coli. The recombinant lipase was purified to homogeneity using ammonium sulfate precipitation, anion-exchange chromatography (Poros 20 HQ) and Sephacryl S-200HR. The molecular mass was shown to be 43 209 Da by mass spectrometry. Crystals suitable for X-ray diffraction analysis were obtained by the hanging-drop method of vapour diffusion with ammonium sulfate as the precipitating agent. Determination of the structure by molecular replacement with existing mesophilic lipase structures has proved unrewarding, as there is less than 20% sequence identity with known lipase structures, but preliminary results with heavy-atom soaking indicate that this strategy will allow the structure to be solved. The availability of this new lipase structure will be of particular significance because it will be the first thermostable lipase to be described.

Amino Acid Sequence↗

PubMedDate not supplied

Analysis of lectin-bound glycoproteins in snake venom from the Elapidae and Viperidae families.

This paper describes an efficient method of studying the glycoproteins found in snake venom. The glycosylation profiles of the Elapidae and Viperidae snake families were analyzed using FITC-labeled lectin glycoconjugates. The Con A-agarose affinity enrichment technique was used to fractionate glycoproteins from the N. naja kaouthia venom. The results revealed a large number of Con A binding glycoproteins, most of which have moderate to high molecular weights. To identify the proteins, the isolated glycoprotein fractions were subjected to two-dimensional electrophoresis and MALDI-TOF MS. Protein sequences were compared with published protein databases to determine for their biological functions.

Animals↗