Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin

Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.

Characterization of interaction property of multicomponents in Chinese Herb with protein by microdialysis combined with HPLC

Interaction of traditional Chinese Herb Rhizoma Chuanxiong and protein was studied by microdialysis coupled with high performance liquid chromatography. Compounds in Rhizoma Chuanxiong, such as ferulic acid, senkyunolide A and 3-butylphthalide, were identified by HPLC, HPLC-MS and UV-vis. Microdialysis recoveries and binding degrees of compounds in Rhizoma Chuanxiong with human serum albumin (HSA) and other human plasma protein were determined: recoveries of microdialysis sampling ranged from 36.7 to 98.4% with R.S.D. below 3.1%; while binding to HSA ranged from 0 to 91.5% (0.3 mM HSA) and from 0 to 93.5% (0.6 mM HSA), respectively. Compared with HSA, most of compounds bound to human blood serum more extensively and the results showed that binding of these compounds in Rhizoma Chuanxiong was influenced by pH. Two compounds were found to bind to HSA and human blood serum. their binding degrees were consistent with ferulic acid and 3-butylphthalide, the active compounds in Rhizoma Chuanoxiong. (c) 2005 Elsevier B.V. All rights reserved.

The complex kinetics of protein folding in wide temperature ranges

The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T-0 is found to be smaller than the folding transition temperature T-f. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal behavior, from high-temperature exponential Poissonian kinetics to the relatively low-temperature highly nonexponential kinetics. The transition temperature is at T-k and T-0, T-k, T-f. In certain low-temperature regimes, a power law behavior at long time emerges. At very low temperatures ( lower than trapping transition temperature T< T-0/(4&SIM;6)), the kinetics is an exponential Poissonian process again.

Drug-protein interaction studied by technique of microdialysis combined with high performance liquid chromatography

Drug-protein binding is an important process in determining the activity and fate of a pharmaceutical agent once it has entered the body. This review examines the method of microdialysis combined with high-performance liquid chromatography (HPLC) that has been developed;by ours to study such interactions, in which the microdialysis was applied to sample the free drug in the mixed solution of drug with protein, and HPLC to quantify the concentration of free drug in the microdialysate. This technique has successfully been used for determining various types of binding interactions between the low affinity drugs, high affinity drugs and enantiomers to HSA. For the case of competitive binding of two drugs to a protein in solution, a displacement equation has been derived and examined with four nonsteroidal anti-inflammatory drugs and HSA as model drugs and protein, respectively. Microdialysis with HPLC was adopted to determine simultaneously the free solute and displacing agent in drug-protein solutions. The method is able to locate the binding site and determine affinity constants even up to 10(7) L/mol accurately.

Modeling of protein adsorption in membrane affinity chromatography

For the design of affinity membranes, protein adsorption in membrane affinity chromatography (MAC) was studied by frontal analysis. According to fast mass transfer, small thickness of affinity membranes and high affinity between the protein and the ligand, an ideal adsorption (IA) model was proposed for MAC and was used together with equilibrium-dispersive (E-D) model to describe the adsorption of bovine serum albumin (BSA) onto cellulose diacetate/polyethyleneimine (CA/PEI) blend membranes with and without Cu2+ chelating. E-D model was found to better describe the initial region of experimental breakthrough curves. The influence of axial dispersion was revealed and it showed the importance of design of the module to homogenously distribute feed solution. IA model was found to be better for the whole experimental breakthrough curve. According to it, the capacity of affinity membranes and the specificity of the interaction are of equal importance for the design of affinity membranes. An optimum feed concentration was also found in the operation of MAC. The discrepancy between experimental optimum feed concentrations and predicted ones from IA model may be due to the ignorance of some experimental effects such as axial dispersion.

The Fluid Phenomena In the Crystallization Of the Protein Crystal

This paper reports that an optical diagnostic system consisting of Mach-Zehnder interferometer with a phase shift device and image processor has been used for study of the kinetics of protein crystal growing process. The crystallization process of protein crystal by vapour diffusion is investigated. The interference fringes are observed in real time. The present experiment demonstrates that the diffusion and the sedimentation influence the crystallization of protein crystal which grows in solution, and the concentration capillary convection associated with surface tension occurs at the vicinity of free surface of the protein mother liquor, and directly affects on the outcome of protein crystallization. So far the detailed analysis and the important role of the fluid phenomena in protein crystallization have been discussed a little in both space- and ground-based crystal growth experiments. It is also found that these fluid phenomena affect the outcome of protein crystallization, regular growth, and crystal quality. This may explain the fact that many results of space-based investigation do not show overall improvement.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Molecular evolution of CXCR1, a G protein-coupled receptor involved in signal transduction of neutrophils

Human neutrophils are a type of white blood cell, which forms an early line of defense against bacterial infections. Neutrophils are highly responsive to the chemokine, interleukin-8 (IL-8) due to the abundant distribution of CXCR1, one of the IL-8 receptors on the neutrophil cell surface. As a member of the GPCR family, CXCR1 plays a crucial role in the IL-8 signal transduction pathway in neutrophils. We sequenced the complete coding region of the CXCR1 gene in worldwide human populations and five representative nonhuman primate species. Our results indicate accelerated protein evolution in the human lineage, which was likely caused by Darwinian positive selection. The sliding window analysis and the codon-based neutrality test identified signatures of positive selection at the N-terminal ligand/receptor recognition domain of human CXCR1.

Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair

Background: Hair is unique to mammals. Keratin associated proteins (KRTAPs), which contain two major groups: high/ultrahigh cysteine and high glycine-tyrosine, are one of the major components of hair and play essential roles in the formation of rigid and