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1.
Magnetization transfer from laser-polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein 下载免费PDF全文
Landon C Berthault P Vovelle F Desvaux H 《Protein science : a publication of the Protein Society》2001,10(4):762-770
Nonspecific lipid transfer protein from wheat is studied by liquid-state NMR in the presence of xenon. The gas-protein interaction is indicated by the dependence of the protein proton chemical shifts on the xenon pressure and formally confirmed by the first observation of magnetization transfer from laser-polarized xenon to the protein protons. Twenty-six heteronuclear nOes have allowed the characterization of four interaction sites inside the wheat ns-LTP cavity. Their locations are in agreement with the variations of the chemical shifts under xenon pressure and with solvation simulations. The richness of the information obtained by the noble gas with a nuclear polarization multiplied by approximately 12,000 makes this approach based on dipolar cross-relaxation with laser-polarized xenon promising for probing protein hydrophobic pockets at ambient pressure. 相似文献
2.
Xenon-binding sites in proteins have led to a number of applications of xenon in biochemical and structural studies. Here we further develop the utility of 129Xe NMR in characterizing specific xenon-protein interactions. The sensitivity of the 129Xe chemical shift to its local environment and the intense signals attainable by optical pumping make xenon a useful NMR reporter of its own interactions with proteins. A method for detecting specific xenon-binding interactions by analysis of 129Xe chemical shift data is illustrated using the maltose binding protein (MBP) from Escherichia coli as an example. The crystal structure of MBP in the presence of 8atm of xenon confirms the binding site determined from NMR data. Changes in the structure of the xenon-binding cavity upon the binding of maltose by the protein can account for the sensitivity of the 129Xe chemical shift to MBP conformation. 129Xe NMR data for xenon in solution with a number of cavity containing phage T4 lysozyme mutants show that xenon can report on cavity structure. In particular, a correlation exists between cavity size and the binding-induced 129Xe chemical shift. Further applications of 129Xe NMR to biochemical assays, including the screening of proteins for xenon binding for crystallography are considered. 相似文献
3.
Duff AP Trambaiolo DM Cohen AE Ellis PJ Juda GA Shepard EM Langley DB Dooley DM Freeman HC Guss JM 《Journal of molecular biology》2004,344(3):599-607
Potential dioxygen-binding sites in three Cu amine oxidases have been investigated by recording X-ray diffraction data at 1.7-2.2A resolution for crystals under a high pressure of xenon gas. Electron-density difference maps and crystallographic refinement provide unequivocal evidence for a number of Xe-binding sites in each enzyme. Only one of these sites is present in all three Cu amine oxidases studied. Structural changes elsewhere in the protein molecules are insignificant. The results illustrate the use of xenon as a probe for cavities, in which a protein may accommodate a dioxygen molecule. The finding of a potential dioxygen-binding cavity close to the active site of Cu amine oxidases may be relevant to the function of the enzymes, since the formation of a transient protein-dioxygen complex is a likely step in the catalytic mechanism. No evidence was found for xenon binding in a region of the molecule that was previously identified in two other Cu amine oxidases as a potential transient dioxygen-binding site. 相似文献
4.
The method for extracting Triton X-100 used by I. H. Mather and C. B. Tampling [Anal. Biochem. 93, 139-142 (1979)], has been extended to other detergents of different charge and chemical nature. All the detergents tested can be extracted with isopentanol in conditions in which not more than 8% of hydrophobic or hydrophilic protein is lost from the water phase. The removal of detergent from reaction centers and light harvesting protein-pigment complexes of photosynthetic bacteria, eliminates the artifacts of oligomers when analyzed by sodium dodecyl sulfate-gel electrophoresis. 相似文献
5.
Veerasamy Jayaraj Ramamoorthi Suhanya Marimuthu Vijayasarathy Perumal Anandagopu Ekambaram Rajasekaran 《Bioinformation》2009,3(9):409-412
Large Hydrophobic Residues (LHR) such as phenylalanine, isoleucine, leucine, methionine and valine play an important rolein protein structure and activity. We describe the role of LHR in complete set of protein sequences in 15 different species.That is the distribution of LHR in different proteins of different species is reported. It is observed that the proteins prefer tohave 27% of large hydrophobic residues in total and all along the sequence. It is also observed that proteins accumulate moreLHR in its active sites. A window analysis on these protein sequences shows that the 27% of LHR is more frequent atwindow length of 45 amino acids. The influenza virus and P. falciparum show a random distribution of LHR in its proteinscompared to other model organisms. 相似文献
6.
Rabi A Musah Gerard M Jensen Steven W Bunte Robin J Rosenfeld David B Goodin 《Journal of molecular biology》2002,315(4):845-857
Cavity complementation has been observed in many proteins, where an appropriate small molecule binds to a cavity-forming mutant. Here, the binding of compounds to the W191G cavity mutant of cytochrome c peroxidase is characterized by X-ray crystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, the W191G cavity does not bind neutral or hydrophobic compounds, but displays a strong specificity for heterocyclic cations, consistent with the role of the protein to stabilize a tryptophan radical at this site. Ligand dissociation constants for the protonated cationic state ranged from 6 microM for 2-amino-5-methylthiazole to 1 mM for neutral ligands, and binding was associated with a large enthalpy-entropy compensation. X-ray structures show that each of 18 compounds with binding behavior bind specifically within the artificial cavity and not elsewhere in the protein. The compounds make multiple hydrogen bonds to the cavity walls using a subset of the interactions seen between the protein and solvent in the absence of ligand. For all ligands, every atom that is capable of making a hydrogen bond does so with either protein or solvent. The most often seen interaction is to Asp235, and most compounds bind with a specific orientation that is defined by their ability to interact with this residue. Four of the ligands do not have conventional hydrogen bonding atoms, but were nevertheless observed to orient their most polar CH bond towards Asp235. Two of the larger ligands induce disorder in a surface loop between Pro190 and Asn195 that has been identified as a mobile gate to cavity access. Despite the predominance of hydrogen bonding and electrostatic interactions, the small variation in observed binding free energies were not correlated readily with the strength, type or number of hydrogen bonds or with calculated electrostatic energies alone. Thus, as with naturally occurring binding sites, affinities to W191G are likely to be due to a subtle balance of polar, non-polar, and solvation terms. These studies demonstrate how cavity complementation and judicious choice of site can be used to produce a protein template with an unusual ligand-binding specificity. 相似文献
7.
Automatic identification and representation of protein binding sites for molecular docking. 总被引:1,自引:0,他引:1 下载免费PDF全文
J. Ruppert W. Welch A. N. Jain 《Protein science : a publication of the Protein Society》1997,6(3):524-533
Molecular docking is a popular way to screen for novel drug compounds. The method involves aligning small molecules to a protein structure and estimating their binding affinity. To do this rapidly for tens of thousands of molecules requires an effective representation of the binding region of the target protein. This paper presents an algorithm for representing a protein's binding site in a way that is specifically suited to molecular docking applications. Initially the protein's surface is coated with a collection of molecular fragments that could potentially interact with the protein. Each fragment, or probe, serves as a potential alignment point for atoms in a ligand, and is scored to represent that probe's affinity for the protein. Probes are then clustered by accumulating their affinities, where high affinity clusters are identified as being the "stickiest" portions of the protein surface. The stickiest cluster is used as a computational binding "pocket" for docking. This method of site identification was tested on a number of ligand-protein complexes; in each case the pocket constructed by the algorithm coincided with the known ligand binding site. Successful docking experiments demonstrated the effectiveness of the probe representation. 相似文献
8.
Two trifluoperazine-binding sites on calmodulin predicted from comparative molecular modeling with troponin-C 总被引:1,自引:0,他引:1
Among the known regulatory proteins that are conformationally sensitive to the binding of calcium ions, calmodulin and troponin-C have the greatest primary sequence homology. This observation has led to the conclusion that the most accurate predicted molecular model of calmodulin would be based on the X-ray crystallographic coordinates of the highly refined structure of turkey skeletal troponin-C. This paper describes the structure of calmodulin built from such a premise. The resulting molecular model was subjected to conjugate gradient energy minimization to remove unacceptable intramolecular non-bonded contacts. In the analysis of the resulting structure, many features of calmodulin, including the detailed conformation of the Ca2+-binding loops, the amino- and carboxy-terminal hydrophobic patches of the Ca2+-bound form, and the several clusters of acidic residues can be reconciled with much of the previously published solution data. Calmodulin is missing the N-terminal helix characteristic of troponin-C. The deletion of three residues from the central helical linker (denoted D/E in troponin-C) shortens the molecule and changes the orientation of the two domains of calmodulin by 60 degrees relative to those in troponin-C. The molecular model has been used to derive two possible binding sites for the antipsychotic drug trifluoperazine, a potent competitive inhibitor of calmodulin activity. 相似文献
9.
Simulating the minimum core for hydrophobic collapse in globular proteins. 总被引:1,自引:1,他引:1 下载免费PDF全文
J. Tsai M. Gerstein M. Levitt 《Protein science : a publication of the Protein Society》1997,6(12):2606-2616
To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling of the cluster formation observed by simulation indicates that this aggregation is cooperative and that the simulations favor the formation of a single cluster midway through the transition stage. This defines a minimum solute hydrophobic core volume. We compare this with protein hydrophobic core volumes determined from solved crystal structures. Our analysis shows that the solute core volume roughly estimates the minimum core size required for independent hydrophobic stabilization of a protein and defines a limiting concentration of nonpolar residues that can cause hydrophobic collapse. These results suggest that the physical forces driving aggregation of hydrophobic molecules in water is indeed responsible for protein folding. 相似文献
10.
Frank C. Greene 《Journal of Protein Chemistry》1984,3(2):167-180
A family of fluorescent probes, consisting of 2-p-toluidinylnapththalene-6-sulfonate (TNS) and neutral and cationic sulfonamido derivatives has been utilized to study the influence of electrostatic forces in protein-amphiphile interactions. 2-p-Toluidinylnaphthalene-6-[N--ethylammonium chloride] sulfonamide (III) binds to a lower number of discrete sites in bovine serum albumin and sperm whale apomyoglobin than does TNS, and is also bound less efficiently by -lactoglobulin. The fluorescence characteristics of the bound probes indicate that their environments are hydrophobic, but thatpH and ionic strength influence the binding. The initial binding of III to discrete sites on both apomyoglobin and bovine serum albumin induces the cooperative binding of additional probe molecules. TNS, but not III, fluoresces in -chymotrypsin solutions. An [N--ethyltrimethyl ammonium] sulfonamido derivative (IV), but not TNS, fluoresces in bovine trypsin solutions. Fluorescence-enhancing interactions were detected between TNS, III, and polyvinylpyrrolidone, but not between these probes and ribonuclease A, -chymotrypsinogen, lysozyme, or -globulins. The wheat prolamin A-gliadin binds more TNS than III. The accessibility of all binding sites of gliadin is lower atpH 5.0 than atpH 3.1. It is suggested that, in general, charge effects are more likely to enhance the binding of anionic than cationic amphibiles by proteins.Dedicated to my teacher, Prof. Robert E. Feeney, on the occasion of his 70th Birthday. Presented in part at the Symposium on Chemical Modification and Structure-Function Relationships of Macromolecules, Division of Agricultural and Food Chemistry, 186th National Meeting of the American Chemical Society, 30 August 1983, Washington, D.C. 相似文献
11.
A prerequisite for NMR studies of protein-ligand interactions or protein dynamics is the assignment of backbone resonances. Here we demonstrate that protein assignment can significantly be enhanced when experimental dipolar couplings (RDCs) are matched to values back-calculated from a known three-dimensional structure. In case of small proteins, the program MARS allows assignment of more than 90% of backbone resonances without the need for sequential connectivity information. For bigger proteins, we show that the combination of sequential connectivity information with RDC-matching enables more residues to be assigned reliably and backbone assignment to be more robust against missing data. Structural or dynamic deviations from the employed 3D coordinates do not lead to an increased error rate in RDC-supported assignment. RDC-enhanced assignment is particularly useful when chemical shifts and sequential connectivity only provide a few reliable assignments. 相似文献
12.
Butyl-Toyopearl 650, a butyl derivative of Toyopearl HW-65, was synthesized for use in hydrophobic chromatography. Water-soluble enzyme proteins were adsorbed on butyl-Toyopearl 650 in the presence of ammonium sulfate and eluted easily in the absence of the salt. Cytochrome c, myoglobin, and chymotrypsinogen A were successfully separated on a butyl-Toyopearl 650 column in order of their individual hydrophobicity by decreasing the concentration of ammonium sulfate contained in the buffer eluant. Based on these results, the use of butyl-Toyopearl 650 is demonstrated for the hydrophobic separation of water-soluble enzyme proteins. 相似文献
13.
Shi Y Fan DJ Li SX Zhang HJ Perrett S Zhou JM 《Protein science : a publication of the Protein Society》2007,16(6):1165-1175
Trigger factor (TF) is the first chaperone to interact with nascent chains and facilitate their folding in bacteria. Escherichia coli TF is 432 residues in length and contains three domains with distinct structural and functional properties. The N-terminal domain of TF is important for ribosome binding, and the M-domain carries the PPIase activity. However, the function of the C-terminal domain remains unclear, and the residues or regions directly involved in substrate binding have not yet been identified. Here, a hydrophobic probe, bis-ANS, was used to characterize potential substrate-binding regions. Results showed that bis-ANS binds TF with a 1:1 stoichiometry and a K(d) of 16 microM, and it can be covalently incorporated into TF by UV-light irradiation. A single bis-ANS-labeled peptide was obtained by tryptic digestion and identified by MALDI-TOF mass spectrometry as Asn391-Lys392. In silico docking analysis identified a single potential binding site for bis-ANS on the TF molecule, which is adjacent to this dipeptide and lies in the pocket formed by the C-terminal arms. The bis-ANS-labeled TF completely lost the ability to assist GAPDH or lysozyme refolding and showed increased protection toward cleavage by alpha-chymotrypsin, suggesting blocking of hydrophobic residues. The C-terminal truncation mutant TF389 also showed no chaperone activity and could not bind bis-ANS. These results suggest that bis-ANS binding may mimic binding of a substrate peptide and that the C-terminal region of TF plays an important role in hydrophobic binding and chaperone function. 相似文献
14.
Proteins in the intracellular lipid-binding protein (iLBP) family show remarkably high structural conservation despite their low-sequence identity. A multiple-sequence alignment using 52 sequences of iLBP family members revealed 15 fully conserved positions, with a disproportionately high number of these (n=7) located in the relatively small helical region. The conserved positions displayed high structural conservation based on comparisons of known iLBP crystal structures. It is striking that the beta-sheet domain had few conserved positions, despite its high structural conservation. This observation prompted us to analyze pair-wise interactions within the beta-sheet region to ask whether structural information was encoded in interacting amino acid pairs. We conducted this analysis on the iLBP family member, cellular retinoic acid-binding protein I (CRABP I), whose folding mechanism is under study in our laboratory. Indeed, an analysis based on a simple classification of hydrophobic and polar amino acids revealed a network of conserved interactions in CRABP I that cluster spatially, suggesting a possible nucleation site for folding. Significantly, a small number of residues participated in multiple conserved interactions, suggesting a key role for these sites in the structure and folding of CRABP I. The results presented here correlate well with available experimental evidence on folding of CRABPs and their family members and suggest future experiments. The analysis also shows the usefulness of considering pair-wise conservation based on a simple classification of amino acids, in analyzing sequences and structures to find common core regions among homologues. 相似文献
15.
The rapidly increasing volume of sequence and structure information available for proteins poses the daunting task of determining their functional importance. Computational methods can prove to be very useful in understanding and characterizing the biochemical and evolutionary information contained in this wealth of data, particularly at functionally important sites. Therefore, we perform a detailed survey of compositional and evolutionary constraints at the molecular and biological function level for a large set of known functionally important sites extracted from a wide range of protein families. We compare the degree of conservation across different functional categories and provide detailed statistical insight to decipher the varying evolutionary constraints at functionally important sites. The compositional and evolutionary information at functionally important sites has been compiled into a library of functional templates. We developed a module that predicts functionally important columns (FIC) of an alignment based on the detection of a significant "template match score" to a library template. Our template match score measures an alignment column's similarity to a library template and combines a term explicitly representing a column's residue composition with various evolutionary conservation scores (information content and position-specific scoring matrix-derived statistics). Our benchmarking studies show good sensitivity/specificity for the prediction of functional sites and high accuracy in attributing correct molecular function type to the predicted sites. This prediction method is based on information derived from homologous sequences and no structural information is required. Therefore, this method could be extremely useful for large-scale functional annotation. 相似文献
16.
In this preliminary study hydrophobic interaction chromatography (HIC) is proposed as a good tool in order to detect conformational changes induced by chemical denaturants in two globular proteins, cytochrome C (Cyt C) and myoglobin (MYO). Alterations in protein structure were manifested chromatographically by reproducible changes in peak heights, retention time, and appearance of multiple peaks. The HIC behavior of the two model proteins denatured by guanidinium thyocyanate (GdmSCN) was investigated, keeping constant various concentrations of urea in the mobile phase in a TSK-Gel Phenyl-5PW column (TosoBiosep). Suitable elution conditions provide evidence of the simultaneous presence of two denatured forms in the case of MYO, and sequential different denatured states of Cyt C. 相似文献
17.
Xuan Peng 《Molecular simulation》2017,43(18):1546-1555
We perform a molecular simulation study on adsorption and separation of the noble gases Xe and Kr in silica-templated amorphous mesoporous carbons (CMK) materials. We generate the atomic models of CMK-3 and CMK-5 materials by adsorbing carbon in a model MCM-41 pore. Our carbon structures can capture the surface roughness and the disordered nature of the carbon rods and carbon pipes as reported in the experiment. The adsorption isotherms and isosteric heats of pure gases have been examined further. We find that the existence of the carbon interconnections between nanorods for CMK-3 and between nanopipes for CMK-5 will reduce the excess uptakes of the noble gases, whereas the isosteric heats are favoured in the materials with interconnections. The carbon interconnections are not advantageous to the adsorption storage of pure gases, but they can improve the separation ability of Xe for gas-mixture adsorption. The effects of temperature and concentration on the Xe separation are investigated and it is shown that the selectivities of Xe in the CMK-5 materials are insensitive to the two factors. We also find that both gas storage and separation of CMK materials are comparable to IRMOF-1 and UMCM-1 metal-organic frameworks. 相似文献
18.
A considerable interest has been put in the identification of biased regions in proteins. These regions are frequently associated with a structural role in the cell and particularly with protein disorder. Here, we have investigated the intrinsically disordered regions (IDRs) in the human charged biased proteins identified in our earlier work. We found that 65% of charged biased proteins contained significant IDRs involved particularly in DNA and RNA binding. Also, we have observed that these proteins are well conserved in metazoans and more particularly in mammalian. In addition, the IDRs are located largely in N-terminal, C-terminal sequence flanking the functional domains (FD) and slightly less in (FD) itself. Our work also supports the association between protein disorder and protein–protein/DNA interaction. An example will be described. 相似文献
19.
Chemical proteomics aims to characterize all of the proteins in the proteome with respect to their function, which is associated with their interaction with other molecules. We propose the identification of a subproteomic library of expressed proteins whose native structures are typified by the presence of hydrophobic surface sites, which are often involved in interactions with small molecules, membrane lipids, and other proteins, pertaining to their functions. We demonstrate that soluble globular proteins with hydrophobic surface sites can be detected selectively by staining on an electrophoretic gel run under nondenaturing conditions. The application of these staining techniques may help elucidate new catalytic, transport, and regulatory functionalities in complex proteomic screenings. 相似文献
20.
Dante M. Beltramo Mariana Nuñez Alejandra del C. Alonso Héctor S. Barra 《Molecular and cellular biochemistry》1994,141(1):57-63
Brain membrane preparations contain tubulin that can be extracted with Triton X-114. After the extract is allowed to partition, 8% of the total brain tubulin is isolated as a hydrophobic compound in the detergent-rich phase. Cytosolic tubulin does not show this hydrophobic behaviour since it is recovered in the aqueous phase. Membrane tubulin can be released by 0.1 M Na2CO3 treatment at pH11.5 in such a way that the hydrophobic tubulin is converted into the hydrophilic form. These results suggest that tubulin exists associated with some membrane component that confers the hydrophobic behaviour to tubulin. If the tissue is homogenized in microtubule-stabilizing buffer containing Triton X-100, the hydrophobic tubulin is isolated from the microtubule fraction. This result indicates that the hydrophobic tubulin isolated from membrane preparations belongs to microtubules thatin vivo are associated to membranes. Therefore, hydrophobic tubulin (tubulin-membrane component complex) can be obtained from membranes or from microtubules depending on the conditions of brain homogenization.Abbreviations TBS
Tris-buffered saline
- Mes
2-(N-morpholine) ethane sulfonic acid 相似文献