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81.
Hermida-Ramón JM Brdarski S Karlström G Berg U 《Journal of computational chemistry》2003,24(2):161-176
An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol. 相似文献
82.
《Chemphyschem》2003,4(4):359-365
We studied the thermodynamic stability of a small monomeric protein, staphylococcal nuclease (Snase), as a function of both temperature and pressure, and expressed it as a 3D free‐energy surface on the p,T‐plane using a second‐order Taylor expansion of the Gibbs free‐energy change ΔG upon unfolding. We took advantage of a series of different techniques (small‐angle Xray scattering, Fourier‐transform infrared spectroscopy, differential thermal analysis, pressure perturbation calorimetry and densitometry) in the evaluation of the conformation of the protein and in evaluating the changes in the thermodynamic parameters upon unfolding, such as the heat capacity, enthalpy, entropy, volume, isothermal compressibility and expansivity. The calculated results of the free‐energy landscape of the protein are in good agreement with experimental data of the p,T‐stability diagram of the protein over a temperature range from 200 to 400 K and at pressures from ambient pressure to 4000 bar. The results demonstrate that combined temperature–pressure‐dependent studies can help delineate the free‐energy landscape of proteins and hence help elucidate which features and thermodynamic parameters are essential in determining the stability of the native conformational state of proteins. The approach presented may also be used for studying other systems with so‐called re‐entrant or Tamman loop‐shaped phase diagrams. 相似文献
83.
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. 相似文献
84.
Villanueva J Villegas V Querol E Avilés FX Serrano L 《Journal of mass spectrometry : JMS》2002,37(9):974-984
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. 相似文献
85.
Syntheses and spectral characteristics of cadmium(II) compounds (CdSeO4, CdSeO3, and Cd(NCSe)2(nia)2) containing selenium in oxidation states (VI), (IV), and (-II) are described. In Cd(NCSe)2(nia)2, nicotinamide (nia) and selenocyanate anions are bonded to Cd atom as N-donor monodentate ligands. Nicotinamide is coordinated
through the ring nitrogen atom. The effects of these selenium compounds as well as Cd(NCS)2(nia)2 on the growth and Cd accumulation in roots and shoots of hydroponically cultivated chamomile plants (cultivar Lutea) were studied. In the applied concentration range (12–60 μmol dm−3) Cd(NCS)2(nia)2 affected neither the length nor the dry mass of roots and shoots. Other compounds applied at 24 μmol dm−3 and 60 μmol dm−3 significantly reduced dry mass of roots and shoots. Selenium oxidation state in the cadmium compounds affected Cd accumulation
in plant organs as well as Cd translocation within the plants, which was reflected in the values of bioaccumulation (BAF)
and translocation factors (S/R). Cd amount accumulated by shoots was lower than that in the roots. The highest BAF values
determined for Cd accumulation in shoots were obtained with CdSeO4. Substitution of S with Se in the Cd(NCX)2(nia)2 (X = Se or S) caused an increase of Cd translocation into the shoots.
Presented at the XVIIIth Slovak Spectroscopic Conference, Spišská Nová Ves, 15–18 October 2006. 相似文献
86.
De La Rosa Luis B. Reshamwala Sultan Latimer Vivian M. Shawky Bahaa T. Dale Bruce E. Stuart Earnest D. 《Applied biochemistry and biotechnology》1994,(1):483-497
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. 相似文献
87.
Grell E. Lewitzki E. Schacht A. Stolz M. 《Journal of Thermal Analysis and Calorimetry》2004,77(2):471-481
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. 相似文献
88.
Guryca V Pacáková V Tlust'áková M Stulík K Michálek J 《Journal of separation science》2004,27(13):1121-1129
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. 相似文献
89.
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. 相似文献
90.