AnalizaDx Inc.

Cleveland, OH, United States

AnalizaDx Inc.

Cleveland, OH, United States

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Fedotoff O.,AnalizaDx Inc. | Mikheeva L.M.,AnalizaDx Inc. | Chait A.,AnalizaDx Inc. | Uversky V.N.,University of South Florida | And 2 more authors.
Journal of Biomolecular Structure and Dynamics | Year: 2012

Partition behavior of prostate-specific antigen (PSA) was studied in aqueous Dextran-Ficoll two-phase system. It was found that the partitioning of PSA changed in the presence of other proteins, in particular, bovine serum albumin, human serum albumin, human transferrin, and human gamma-globulin. The partition coefficient of PSA in mixtures with increasing amounts of these proteins decreased along the S-shaped curve and dropped to essentially the same value at the 10 4-10 5 protein: PSA molar ratio. Partition behavior of the above proteins was examined separately. Partition coefficient of a protein represents the protein solvent exposed residues; i.e., it reflects the 3D-structure of the protein in solution. Partition of binary protein mixtures reflects the interaction of the two proteins and therefore characterizes the PSA-induced conformational changes in a protein agent and the change in the PSA conformation induced by a protein agent. In other words, the protein effect on the partition behavior of free PSA may be explained by the effect of the non-specific PSA-protein interactions on PSA conformation. Formation of such PSA-protein encounter complexes was shown to be dominated by the electrostatic forces, since the efficiency of a given protein-agent to induce changes in the partition behavior of PSA was proportional to its absolute mean net charge. Furthermore, in agreement with the earlier hypothesis that the protein segments with increased dynamic propensities (i.e., 'discrete breathers') can be important for conformational transitions accompanying binding processes, our analysis of intrinsically disordered regions (IDR) in all the proteins examined showed that the propensity for intrinsic disorder is related to the PSA partition-modulating capability of the protein. ©Adenine Press (2012).


Madeira P.P.,University of Porto | Bessa A.,University of Porto | Loureiro J.A.,University of Porto | Alvares-Ribeiro L.,University of Porto | And 2 more authors.
Journal of Chromatography A | Year: 2015

Partition coefficients of seven low molecular weight compounds were measured in multiple aqueous two-phase systems (ATPSs) formed by pairs of different polymers. The ionic composition of each ATPS was varied to include 0.01M sodium phosphate buffer (NaPB), pH 7.4 and 0.1M Na2SO4, 0.15M NaCl, and 0.15M NaClO4 all in 0.01M NaPB, pH 7.4. The differences between the solvent features of the coexisting phases in all the ATPSs were estimated from partitioning of a homologous series of dinitrophenylated-amino acids and by the solvatochromic method. The solute-specific coefficients for the compounds examined were determined by the multiple linear regression analysis using the modified linear solvation energy relationship equation. It is established that the solute specific coefficients characterizing different types of the solute-water interactions (dipole-dipole, dipole-ion, and H-bonding) for a given solute change in the presence of different salt additives in the solute specific manner. It is also found that these characteristics are linearly interrelated. It is suggested that there is a cooperativity between various types of solute-water interactions governed by the solute structure. © 2015 Elsevier B.V.


Ferreira L.A.,AnalizaDx Inc. | Madeira P.P.,University of Porto | Uversky A.V.,Temple University | Uversky V.N.,University of South Florida | And 3 more authors.
Journal of Chromatography A | Year: 2015

Protein partitioning in aqueous two-phase systems (ATPS) is widely used as a convenient, inexpensive, and readily scaled-up separation technique. Protein partition behavior in ATPS is known to be readily manipulated by ionic composition. However, the available data on the effects of salts and buffer concentrations on protein partitioning are very limited. To fill this gap, partitioning of 15 proteins was examined in dextran-poly(ethylene glycol) ATPSs with different salt additives (Na2SO4, NaClO4, NaSCN, CsCl) in 0.11M sodium phosphate buffer, pH 7.4. This analysis reveals that there is a linear relationship between the logarithms of the protein partition coefficients determined in the presence of different salts. This relationship suggests that the protein response to ionic environment is determined by the protein structure and type and concentrations of the ions present. Analysis of the differences between protein structures (described in terms of proteins responses to different salts) and that of cytochrome c chosen as a reference showed that the peculiarities of the protein surface structure and B-factor used as a measure of the protein flexibility are the determining parameters. Our results provide better insight into the use of different salts in manipulating protein partitioning in aqueous two-phase systems. These data also demonstrate that the protein responses to different ionic environments are interrelated and are determined by the structural peculiarities of protein surface. It is suggested that changes in ionic microenvironment of proteins may regulate protein transport and behavior in biological systems. © 2015 Elsevier B.V.


Uversky V.N.,University of South Florida | Uversky V.N.,Russian Academy of Sciences | Kuznetsova I.M.,Saint Petersburg State Polytechnic University | Turoverov K.K.,Saint Petersburg State Polytechnic University | Zaslavsky B.,AnalizaDx Inc.
FEBS Letters | Year: 2015

Here, we hypothesize that intrinsically disordered proteins (IDPs) serve as important drivers of the intracellular liquid-liquid phase separations that generate various membrane-less organelles. This hypothesis is supported by the overwhelming abundance of IDPs in these organelles. Assembly and disassembly of these organelles are controlled by changes in the concentrations of IDPs, their posttranslational modifications, binding of specific partners, and changes in the pH and/or temperature of the solution. Each resulting phase provides a distinct solvent environment for other solutes leading to their unequal distribution within phases. The specificity and efficiency of such partitioning is determined by the nature of the IDP(s) and defines "targeted" enrichment of specific molecules in the resulting membrane-less organelles that determines their specific activities. © 2014 Federation of European Biochemical Societies.


Ferreira L.,AnalizaDx Inc. | Madeira P.P.,University of Porto | Mikheeva L.,AnalizaDx Inc. | Uversky V.N.,University of South Florida | And 2 more authors.
Biochimica et Biophysica Acta - Proteins and Proteomics | Year: 2013

Partitioning of 15 proteins in polyethylene glycol (PEG)-sodium sulfate aqueous two-phase systems (ATPS) formed by PEG of two different molecular weights, PEG-600 and PEG-8000 in the presence of different buffers at pH 7.4 was studied. The effect of two salt additives (NaCl and NaSCN) on the protein partition behavior was examined. The salt effects on protein partitioning were analyzed by using the Collander solvent regression relationship between the proteins partition coefficients in ATPS with and without salt additives. The results obtained show that the concentration of buffer as well as the presence and concentration of salt additives affects the protein partition behavior. Analysis of ATPS in terms of the differences between the relative hydrophobicity and electrostatic properties of the phases does not explain the protein partition behavior. The differences between protein partitioning in PEG-600-salt and PEG-8000-salt ATPS cannot be explained by the protein size or polymer excluded volume effect. It is suggested that the protein-ion and protein-solvent interactions in the phases of ATPS are primarily important for protein partitioning. © 2013 Elsevier B.V.


PubMed | AnalizaDx Inc.
Type: Journal Article | Journal: Journal of biomolecular structure & dynamics | Year: 2012

Partition behavior of prostate-specific antigen (PSA) was studied in aqueous Dextran-Ficoll two-phase system. It was found that the partitioning of PSA changed in the presence of other proteins, in particular, bovine serum albumin, human serum albumin, human transferrin, and human gamma-globulin. The partition coefficient of PSA in mixtures with increasing amounts of these proteins decreased along the S-shaped curve and dropped to essentially the same value at the 10(4)-10(5) protein: PSA molar ratio. Partition behavior of the above proteins was examined separately. Partition coefficient of a protein represents the protein solvent exposed residues; i.e., it reflects the 3D-structure of the protein in solution. Partition of binary protein mixtures reflects the interaction of the two proteins and therefore characterizes the PSA-induced conformational changes in a protein agent and the change in the PSA conformation induced by a protein agent. In other words, the protein effect on the partition behavior of free PSA may be explained by the effect of the non-specific PSA-protein interactions on PSA conformation. Formation of such PSA-protein encounter complexes was shown to be dominated by the electrostatic forces, since the efficiency of a given protein-agent to induce changes in the partition behavior of PSA was proportional to its absolute mean net charge. Furthermore, in agreement with the earlier hypothesis that the protein segments with increased dynamic propensities (i.e., discrete breathers) can be important for conformational transitions accompanying binding processes, our analysis of intrinsically disordered regions (IDR) in all the proteins examined showed that the propensity for intrinsic disorder is related to the PSA partition-modulating capability of the protein.


PubMed | AnalizaDx Inc.
Type: Journal Article | Journal: Biochimica et biophysica acta | Year: 2013

Partitioning of 15 proteins in polyethylene glycol (PEG)-sodium sulfate aqueous two-phase systems (ATPS) formed by PEG of two different molecular weights, PEG-600 and PEG-8000 in the presence of different buffers at pH7.4 was studied. The effect of two salt additives (NaCl and NaSCN) on the protein partition behavior was examined. The salt effects on protein partitioning were analyzed by using the Collander solvent regression relationship between the proteins partition coefficients in ATPS with and without salt additives. The results obtained show that the concentration of buffer as well as the presence and concentration of salt additives affects the protein partition behavior. Analysis of ATPS in terms of the differences between the relative hydrophobicity and electrostatic properties of the phases does not explain the protein partition behavior. The differences between protein partitioning in PEG-600-salt and PEG-8000-salt ATPS cannot be explained by the protein size or polymer excluded volume effect. It is suggested that the protein-ion and protein-solvent interactions in the phases of ATPS are primarily important for protein partitioning.


PubMed | AnalizaDx Inc., University of Porto, Russian Academy of Sciences and Temple University
Type: | Journal: Journal of chromatography. A | Year: 2015

Protein partitioning in aqueous two-phase systems (ATPS) is widely used as a convenient, inexpensive, and readily scaled-up separation technique. Protein partition behavior in ATPS is known to be readily manipulated by ionic composition. However, the available data on the effects of salts and buffer concentrations on protein partitioning are very limited. To fill this gap, partitioning of 15 proteins was examined in dextran-poly(ethylene glycol) ATPSs with different salt additives (Na2SO4, NaClO4, NaSCN, CsCl) in 0.11 M sodium phosphate buffer, pH 7.4. This analysis reveals that there is a linear relationship between the logarithms of the protein partition coefficients determined in the presence of different salts. This relationship suggests that the protein response to ionic environment is determined by the protein structure and type and concentrations of the ions present. Analysis of the differences between protein structures (described in terms of proteins responses to different salts) and that of cytochrome c chosen as a reference showed that the peculiarities of the protein surface structure and B-factor used as a measure of the protein flexibility are the determining parameters. Our results provide better insight into the use of different salts in manipulating protein partitioning in aqueous two-phase systems. These data also demonstrate that the protein responses to different ionic environments are interrelated and are determined by the structural peculiarities of protein surface. It is suggested that changes in ionic microenvironment of proteins may regulate protein transport and behavior in biological systems.

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