Structural changes in R-phycoerythrin upon CdS quantum dot synthesis in tunnel cavities of protein molecules.

Structural changes in R-phycoerythrin used as a matrix for the synthesis of CdS quantum dots have been analyzed by circular dichroism spectrometry. In deionized water, quantum dot synthesis in the tunnel cavity of the R-phycoerythrin molecule proved to be accompanied by uncoiling of α-helices and changes in the conformation of its chromophore groups, with consequent decay of protein fluorescence. Since R-phycoerythrin fluorescence is important for practical applications, conditions for quantum dot synthesis have been optimized by replacing deionized water with 0.01 M MES buffer, pH 5.7. Under such conditions, the size of the CdS quantum dots (determined from atomic force microscopy images) remains the same as in deionized water, but quantum dots cause only minor structural changes in protein molecules, as follows from circular dichroism and absorption spectra. The thermostability of R-phycoerythrin is enhanced, as indicated by an increase in the experimental activation energy for denaturation (from 140.8 to 149.9 kJ/mol) and the intensity of R-phycoerythrin fluorescence is also enhanced approximately twofold.

"Prostate cancer proteomics" database.

A database of Prostate Cancer Proteomics has been created by using the results of a proteomic study of human prostate carcinoma and benign hyperplasia tissues, and of some human-cultured cell lines (PCP, http://ef.inbi.ras.ru). PCP consists of 7 interrelated modules, each containing four levels of proteomic and biomedical data on the proteins in corresponding tissues or cells. The first data level, onto which each module is based, is a 2DE proteomic reference map where proteins separated by 2D electrophoresis, and subsequently identified by mass-spectrometry, are marked. The results of proteomic experiments form the second data level. The third level contains protein data from published articles and existing databases. The fourth level is formed with direct Internet links to the information on corresponding proteins in the NCBI and UniProt databases. PCP contains data on 359 proteins in total, including 17 potential biomarkers of prostate cancer, particularly AGR2, annexins, S100 proteins, PRO2675, and PRO2044. The database will be useful in a wide range of applications, including studies of molecular mechanisms of the aetiology and pathogenesis of prostate diseases, finding new diagnostic markers, etc.

Proteomic analysis of human skeletal muscle (m. vastus lateralis) proteins: identification of 89 gene expression products.

Proteins from bioptates and autoptates of human skeletal muscle m. vastus lateralis were separated by O'Farrell two-dimensional gel electrophoresis (2DE). MALDI-TOF MS and MS/MS enabled identification of 89 protein spots as expression products of 55 genes. A modification of the O'Farrell's method including non-equilibrium electrophoresis in a pH gradient allowed detection--among major sarcomeric, mitochondrial, and cytosolic proteins--of several proteins, such as PDZ- and LIM domain-containing ones (pI > 8.70), fragments of known proteins, and a stable complex of heavy and light ferritin chains. The data underlie further studies of human skeletal muscle proteins in terms of molecular mechanisms of some physiological and pathological processes.

Polymorphism of delta3,5-delta2,4-dienoyl-coenzyme A isomerase (the ECH1 gene product protein) in human striated muscle tissue.

Two polymorphic variants of the ECH1 gene product protein (delta3,5-delta2,4-dienoyl-coenzyme A isomerase) have been revealed by proteomics methods in samples of human striated muscle tissue. These variants are identical in molecular weight (29.7 kD) but different in pI values (6.57 and 6.75) and in amino acid substitution (41 E-->A) confirmed by mass spectrometry. The same type of polymorphism has been detected in samples of different tissues of the same person, so these variants are considered (also based on other data) to be allelic. The rates of these alleles in two representative cohorts of Moscow and Minsk residents are similar.

Proteomic studies of human and other vertebrate muscle proteins.

This review summarizes results of some systemic studies of muscle proteins of humans and some other vertebrates. The studies, started after introduction of two-dimensional gel electrophoresis of O'Farrell, were significantly extended during development of proteomics, a special branch of functional genomics. Special attention is paid to analysis of characteristic features of strategy for practical realization of the systemic approach during three main stages of these studies: pre-genomic, genomic (with organizational registration of proteomics), and post-genomic characterized by active use of structural genomics data. Proteomic technologies play an important role in detection of changes in isoforms of various muscle proteins (myosins, troponins, etc.). These changes possibly reflecting tissue specificity of gene expression may underline functional state of muscle tissues under normal and pathological conditions, and such proteomic analysis is now used in various fields of medicine.

A new protein of human atrium.

The partial amino acid sequence (23 amino acid residues) of a protein isolated from human atrium has been determined. The sequence homology shows that this protein belongs to the myosin 1 light chain family (an atrium-specific isoform).

Standardized and extended catalog of major proteins of the human kidney.

A new version of a two-dimensional electrophoretic catalog of proteins of the human kidney and of various morphological and functional structures of the human kidney is presented; it contains information about 179 polypeptides. The following proteins were identified: crystallin, albumin, mitochondrial superoxide dismutase, actin, fatty acid-binding protein, alpha-ATP-synthase, and transferrin. Some protein groups are specific for certain morphological structures.

The major protein expression profile and two-dimensional protein database of human heart.

The construction of a two-dimensional protein database of the human heart is presented. The database contains information on about 300 abundant proteins of human myocardial tissue, including approximately 40 proteins that were identified by different methods. Each protein was characterized according to several parameters, including molecular weight, isoelectric point, name, partial sequence, subcellular localization, and genetic as well as embryonic changes.

Identification of an allelic variant of isoform MLC1-V/sB (human myosin light chain).

A study of 250 specimens of human myocardium by two-dimensional gel electrophoresis revealed an allelic variant of isoform MLC1-V/sB, which was identified by immunoblotting with monoclonal antibody against MLC1-V/sB and peptide mapping after in situ tryptic digestion of electroblotted proteins. The substitution Asn-144 for His-144 was found in this new allelic variant of MLC1-V/sB.

Production of high purity proteins by elution of individual fractions from two-dimensional gels.

Results are presented on the production of purified myocardial proteins from two-dimensional (2-D) gels. Proteins were fixed in a native condition using potassium acetate and then eluted into an aqueous solution. Homogeneous tropomyosin and myosin light chain fractions and a number of nonidentified myocardial proteins present on 2-D gels were obtained.

Two-dimensional electrophoresis of heart muscle proteins in human cardiomyopathies.

Human heart muscle proteins have been analyzed by two-dimensional electrophoresis. Twenty five autopsy heart muscle samples obtained from individuals who had died in accidents and who had no signs of cardiovascular pathology have been compared with biopsy and autopsy myocardium samples of patients with: dilated cardiomyopathy (5 cases), hypertrophical cardiomyopathy (2 cases) and myocarditis (2 cases). In dilated cardiomyopathy in 3 out of 5 cases an additional protein spot was found in the myocardial myosin light chain 1 area.