Incorporation of FT-IR spectral data in a computer-assisted prediction of globular protein structure

Currently, much effort is being directed to the determination of the three-dimensional structure of proteins. Two classes of research are of interest; spectrometric techniques which include Fourier transform infrared (FT-IR) spectrometry, and non-spectrometric prediction schemes. The spectra obtained using FT-IR spectrometry, are analyzed to determine the percentages of alpha-helices, beta-pleated sheets, and non-structured coils in a protein. Unfortunately, FT-IR, as well as other spectrometric techniques, cannot be used to determine the exact secondary structure of a protein reliably. Non-spectrometric prediction methods yield information on the exact secondary structure, but are not always accurate. Most prediction methods relate the primary amino acid sequence to the secondary structure of a protein, allowing sequential secondary structure information for the protein examined to be obtained. The goal of this research is to incorporate FT-IR with a prediction method, resulting in an improvement in the accuracy of the prediction.     

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability.     

Integrated production of ethanol fuel and protein from Coastal Bermudagrass

The herbaceous crops that may provide fermentable carbohydrates for production of fuels and chemicals also contain 10–20% protein. Protein coproduction with biomass-derived fuels and chemicals has important advantages: (1) food and fuel production can be integrated, and (2) protein is a high-value product that may significantly improve overall process economics. We report the results of an integrated approach to producing protein and fermentable sugars from one herbaceous species, Coastal Bermudagrass (CBG). The ammonia fiber explosion (AFEX) process makes possible over 90% conversion of cellulose and hemicellulose to simple sugars (about 650 mg reducing sugars/g dry CBG) at 5 IU cellulase/g vs < 20% conversion for untreated CBG. The AFEX treatment also improves protein extraction from CBG; over 80% protein recovery is possible from AFEX-treated CBG vs about 30% recovery from untreated CBG.     

Nucleotide/Protein Interaction: Energetic and Structural Features of Na,K-ATPase

Microcalorimetric titrations allow to recognize and investigate high-affinity ligand binding to Na,K-ATPase. Titrations with the cardiac glycoside Ouabain, which acts as a specific inhibitor of the enzyme, have provided not only the thermodynamic parameters of high-affinity binding with a stoichiometric coefficient of about 0.6 but also evidence for low-affinity binding to the lipid. The marked enthalpic contribution of -95 kJ mol^-1 at 298.2 K is partially compensated by a large negative entropy change, attributed to an increased interaction between water and the protein. The calorimetric ADP and ATP titrations at 298.2 K are indicative of high-affinity nucleotide binding either in 3 mM NaCl, 3 mM MgCl₂ or at high ionic strength such as 120 mM choline chloride. However, no binding is detected in the buffer solution alone at low ionic strength. The affinities for ADP and ATP are similar, around 10⁶ M^-1 and the stoichiometric coefficients are close to that of Ouabain binding. The exothermic binding of ADP is characterized by a ΔH and ΔS value of -65 kJ mol^-1 and -100 J mol^-1 K^-1, respectively. TheΔH value for ATP binding is larger than for ADP and is compensated by a larger, unfavorable ΔS value. This leads to an enthalpy/entropy compensation, which could express that H-bond formation represents the major type of interaction. As for Ouabain, the negative ΔS values that are also characteristic of nucleotide binding can indicate an increase of solvate interaction with the protein due to a conformational transition occurring subsequent to the binding process. The resulting binding constants are discussed with regard to the results of other studies employing different techniques. A molecular interaction model for nucleotide binding is suggested. This revised version was published online in July 2006 with corrections to the Cover Date.     

Topographical properties of polymer films deposited in capillaries for electrophoretic separations of large organic molecules

Topography and thickness of hydrophilic polymer coatings of fused-silica capillaries for capillary electrophoresis (CE) were investigated using atomic force microscopy (AFM), scanning electron microscopy (SEM), and profilometry. Three hydrogels, poly(2-hydroxyethyl methacrylate) [poly(HEMA)], poly(diethylene glycol monomethacrylate) [poly(DEGMA)], and poly(triethylene glycol monomethacrylate) [poly(TEGMA)], were deposited using two procedures, either by simple physical sorption of the polymers, or by derivatization of the capillary wall surface with glycidyl methacrylate (EPMA) followed by polymerization of the appropriate monomers. The performance of the modified capillaries was tested under CE conditions (decrease in the electroosmotic flow, EOF dependence on pH, separation of milk and standard proteins). It has been found that the most important property of the polymer coating is its thickness, whereas its topography and the degree of its hydrophobicity are less significant. Film deposition by physical adsorption is preferable to polymerization on the derivatized surface.     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

The influence of the pore size, the foaming temperature and the viscosity of the continuous phase on the properties of foams produced by membrane foaming

Membrane foaming is a new method of foaming. To enlarge the knowledge about the influencing factors and to know how to vary the structure of the resulting foam, different factors were evaluated. A whey protein solution with 10% protein was foamed as a model solution by means of a tubular cross-flow filtration membrane. The pore size of the membrane was varied. The smaller the pore size, the smaller the bubbles produced. As a result, the foam firmness increases and less drainage was observed when smaller pore sizes were applied.

An important factor is that the added amount of gas must be stabilised as completely as possible in the foam. In order to achieve this, both the process and the product parameters were varied. Raising the foaming temperature increased the quantity of stabilised gas. The whey proteins then diffuse faster to the bubble surfaces and stabilise these by unfolding and networking reactions to prevent the coalescence of the bubbles.

The product parameter viscosity was found to influence the foaming result in such a way that up to a viscosity of 40 mPa s the incorporated gas bubbles are stabilised by the higher viscosity. At viscosities higher than 40 mPa s it is difficult to incorporate in the bubbles, and the foam structure becomes coarser due to increased coalescence at the pores of the membrane. The foam stability is enhanced with higher viscosities.     

高效液相色谱蛋白质手性固定相

本文综述了近年文献中已报道的各种高效液相色谱蛋白质（酶）手性固定相及其在手性拆分中的应用，并阐述了蛋白质作为手性选择剂拆分机理的研究进展。     

高效毛细管电泳前沿分析法研究酸性药物那格列奈与人血浆白蛋白的结合

用高效毛细管电泳前沿分析法研究了酸性药物那格列奈与人血浆白蛋白的结合常数、结合位点和结合率。使用未涂层的毛细管柱 (4 0cm× 5 0 μmi.d .;有效柱长 32cm) ,磷酸盐缓冲溶液 (pH 7.4 ,离子强度0 .17)为背景溶液 ,在紫外检测波长 2 14nm、运行电压 18kV和重力进样 10 0s的条件下 ,利用那格列奈谱峰的平台高度和游离药物浓度的良好线性关系 (r>0 .999,n =6 ) ,测定了那格列奈的游离药物浓度。固定药物浓度 (2 0 0 μmol L ,2 5 0 μmol L) ,考察不同的蛋白质浓度对结合的影响 ;固定蛋白质浓度 (10 0 μmol L) ,考察不同的药物浓度对结合的影响。实验数据采用非线性拟和程序进行处理 ,得到了那格列奈的蛋白质结合参数。高效毛细管电泳前沿分析法测定的数据重现性良好 (RSD <2 .5 % ,n =3) ,在药代动力学和药效学研究方面具有简便、准确的优点。     

高效前沿分析的发展及在药物-蛋白结合研究中的应用

介绍了高效前沿分析方法的原理、特点、种类，综述了它在药物与蛋白结合研究中的应用及国内外研究概况；通过与高效液相色谱／前沿分析比较，阐明了毛细管电泳／前沿分析在药物蛋白结合研究中的优势；分析了在药物与蛋白结合研究中所采用的各种研究方法，通过与这些研究方法的比较，阐明了高效前沿分析的优越性及其广阔的应用前景，同时提出了在高效前沿分析方法中有待完善和注意的问题。