protein structure and drug discovery

... network and dynamics perspective PLoS One 9: e102856 157 158 Understanding the Structure and Dynamics of Peptides and Proteins 271 Dib, L and Carbone, A (2012) Protein fragments: functional and structural ... Applications 94 Mapping Protein Ligand and Biomedical Studies 94 Enzyme Characterization 96 Acknowledgments 97 References 97 Understanding the Structure and Dynamics of Peptides and Proteins Through ... molecular dynamics: some examples Curr Comput.-Aided Drug Des 9: 532 149 150 Understanding the Structure and Dynamics of Peptides and Proteins 132 Marco, E and Gago, F (2007) Overcoming the inadequacies

Ngày tải lên: 20/01/2020, 09:27

... 238 protein? ??ligand unbinding 87 protein? ??peptide binding 34–36 protein? ??peptide complex 34, 35 protein? ??peptide recognition 34 protein? ? ?protein binding 32–34, 129 protein? ? ?protein complexes 33, 34 protein? ? ?protein ... 174, 182, 183 protein? ??ligand binding 15, 30, 32, 33, 36–38, 87, 175, 227, 230 protein? ??ligand complex 4, 6, 10, 17, 33, 87, 175, 176, 227, 238 protein? ??ligand docking 4, 20 protein? ??ligand interaction ... leucine 329 overexpression and increased ubiquitination 326 from phenotype to structure 331–332 protein sequence and structure 328–329 structure and dynamics 326 Cdc34-like proteins 330 cell cycle

Ngày tải lên: 21/01/2020, 04:21

... evolution) and same function but different fold (convergent evolution) Protein Classification Systems The rapid growth in the number of protein sequences and 3D structures has made it practical and ... two distantly related protein sequences is their underlying structures, or folds Transitivity requires that the well-established relationship between sequence and structure and the more indefinite ... the relationship between protein function and structure We focus initially on enzymes classified by the Enzyme Commission (EC) and relate these to structurally classified proteins in the SCOP database

Ngày tải lên: 18/10/2022, 03:30

... targets and drug of the approved, clinical trial, and experimental drugs. These database lead to a better understanding of the disease and benefit for drug discovery. Src promotes tumour invasion and ... laboratory worker and may contribute to severe diseases or mortality 1.2 Bioinformatics and cheminformatics in drug discovery The combination of random screening and rational drug design ... important role in drug discovery [44] The traditional drug discovery. .. development of web accessible databases for pathogen 11 detection and therapeutic targets and drugs Owing

Ngày tải lên: 10/09/2015, 09:04

... is a putative protein? ? ?protein interaction module Four KIND-containing proteins, Spir-2 (actin-nuclear factor), PTPN13 (protein tyrosine phosphatase), FRMPD2 (scaffold protein) and very-KIND (v-KIND) ... domains of Spir-2 and PTPN13 were generated by RT-PCR and inserted into pEGFP-C1 and pGEX-4T-2 The N- and C-terminal regions of the v-KIND KIND2 and the MAP2 CD were generated by PCR and cloned into ... study revealed the structural and functional determinants of the protein? ? ?protein interaction between v-KIND and MAP2 (i.e the MAP2-binding core module in v-KIND and the v-KIND-binding core module

Ngày tải lên: 14/02/2014, 19:20

... screens and selection for protein stability and structure. ) Cellular expression One straightforward strategy of screening for structured proteins is to make limited or highly biased libraries and then ... lab has studied the structure, function, stability and folding of the four-helix bundle protein rop. Rop is an excellent model system for under- standing protein structure and stability: it can ... X-ray crystallography [38,39] and calorimetry [40] is increasing rapidly for drug discovery and proteomics). However, as a consequence of a native-like protein? ??s stability and structural specificity,

Ngày tải lên: 19/02/2014, 12:20

... alignments: Application to distantly related proteins Proteins 2004, 55:436-454 Shapiro J, Brutlag D: FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web Nucl Acids Res 2004, ... backbone Protein Eng 1999, 12:1063-1073 Hunter CG, Subramaniam S: Protein fragment clustering and canonical local shapes Proteins 2003, 50:580-588 Sander O, Sommer I, Lengauer T: Local protein structure ... combine protein sequence and structure in one framework for protein alignment and comparison Larger scale testing needs to be done to estimate its significance The server is available for structure

Ngày tải lên: 12/08/2014, 17:20

... to fitting procedures, and could be adapted to different drugs and transporters. The physiological based model is novel and unique and brought effective information on drug transporters. Page ... Pglycoprotein assays in drug discovery J Pharmacol Exp Ther 2001, 299:620–628 Stephens RH, O'Neill CA, Bennett J, Humphrey M, Henry B, Rowland M and Warhurst G: Resolution of P-glycoprotein ... permeability, P-glycoprotein transport ratios and brain penetration of heterocyclic drugs Int J Pharm 2003, 263:113– 122 Pang KS and Rowland M: Hepatic clearance of drugs I Theoretical considerations

Ngày tải lên: 13/08/2014, 16:21

... detect, visualize and analyze residue co-locations in and between protein structures [14]. Eighty different protein structures were taken from the protein structure database [15] and residue co-locations ... step of ab initio protein structure prediction (as well as protein design) is the prediction of the secondary structure (i.e. the location and length of alpha helices, beta strands and turns). This ... involved in protein structural uniqueness: implication for de novo protein design Protein Eng 2002, 15:555-560 Brunak S, Engelbrecht J: Protein structure and the sequential structure

Ngày tải lên: 13/08/2014, 23:20

... reliability of a hit protein structure. For the purposes of scanning a large protein structure database, 3D-BLAST is fast and accurate and is useful for the initial scan for similar protein structures, ... groups (Fig- ure 2a and Additional data file 2): helix letters (A, Y, B, C, and D), helix-like letters (G, I, and L), strand letters (E, F, and H), strand-like letters (K and N), and others. The ... query protein and the hit proteins. A total of 22,415 proteins were randomly chosen from the hit lists of 516 query proteins in the SCOP-516 dataset. Among these 22,415 proteins, 27.72% (6,215 structures)

Ngày tải lên: 14/08/2014, 18:20

... Terminal Region Mediates Multiple Protein/ Protein Interactions within the DNA-dependent Protein Kinase Complex: Relating Structure and Function Department of Biochemistry and Molecular Biology Research ... 1) Woods DS and Turchi JJ (2011) The Ku80 Carboxy Terminal Region Mediates Multiple Protein/ Protein Interactions within the DNA-dependent Protein Kinase Complex: Relating Structure and Function ... DNA-PKcs is intimately tied to the protein structure of Ku80 C-terminal regions and the structure of the DNA substrate to which the holoenzyme is bound Thus if DNA structure influences phosphorylation

Ngày tải lên: 24/08/2014, 09:33

... metabolism-relevant ligands Click here data file bio-ligands Ligands and theand2 of bio-ligands and binding ATP, ligands Additionalfor file 1ownerships of metabolism-relevantADP and block numbers of for proteins ... ACD-SC-derived ordinary molecules; Ligands, sc-PDB-derived ligands; Ligands (≤ 3), ligands covering ≤ folds; Ligands (4-9), ligands covering 4-9 folds; Ligands (≥ 10), ligands covering ≥ 10 folds Implications ... ligand (L) Figure Power-law behaviors of ligand -protein binding Power-law behaviors of ligand -protein binding The number of ligands (N) decays with an increase in the number (L) of (a) domains and...

Ngày tải lên: 14/08/2014, 08:20

... diabetic human placenta and then to purify and examine kinetic properties The fresh placenta was obtained and the tissues were cooled, washed and perfused and weighed, then minced and suspended in three ... precursor, huntingtin, parkin and fragile-X mental retardation proteins as well as some S100, IeF, ribosomal, chaperone, receptor, adaptor and serum proteins and several proteins associated with ataxia, ... activity of p53 and the p73 isoforms was then analysed on some of the common and unique targets and the cross-talk between p53 and its family members was also investigated N3-036P Structure and expression...

Ngày tải lên: 23/03/2014, 15:20

... implant testing and drug discovery along its differentiation process toward osteogenic lineage Most of the current implant testing relies on adult stem cell (Mesenchymal stem cells, etc.) and primary ... the implant, but also helps us to understand development of osteoblast cells that constitute the bone and their function In sum, either as a model for drug discovery or implant testing, hESCs are ... potential drugs and medicine without the use of animals or human volunteers Comparing with immortal cell lines and animal models, stem cell reflects the best human physiology When used for drug testing,...

Ngày tải lên: 16/10/2015, 15:38

... hindrance between peptide and protein, and to relax the hydrogen added to the protein, the peptide and protein were merged and minimized before docking Atomic solvation parameters and fragmental volumes ... of hCD2 and rat CD2 3D structures indicated that Tyr86 and Glu36 side chains overlap in hCD2 and rat CD2 and oriented in the same direction in both the structures To stabilize the b-turn structure ... Human-CD2 and rat-CD2 have high 3D structure similarity Comparison of 3D structures of hCD2 from CD2–CD58 complex [30] and the structure of rat CD2 [36] using DS modeling (Accelrys Inc., Sandiego,...

Ngày tải lên: 19/02/2014, 13:20

... between the structures of TLP and transthyretins are found in the loop connecting b-strands B and C, which is highly exposed to the solvent in TLP [17] Interruptions in the b-strands A, G and H are ... S dublin TLP and zebrafish TLP are found in the flexible portions of strands B and C that protrude towards the solvent and in the conformation of the long loop connecting strands D and E [17] Greater ... between the loops joining stands G and H with the loops joining strands A and B, making the transthyretin tetramer a ‘dimer of dimers.’ Recently, the first crystal structures of TLP from various...

Ngày tải lên: 07/03/2014, 00:20

... for protein interaction Protein Sci 13, 2370– 2377 Herrmann T, Guntert P & Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software candid and ... in studying the dynamics of protein structures from 15 N and 13C relaxation time mesurements In Biological Magnetic Resonance: Structure Computation and Dynamics in Protein NMR (Krishna NR & Berliner ... presented in yellow, and the polar and charged surfaces are shown in white HT1 and HT2 are hydrophobic trail and 2, respectively HL denotes the hydrophobic linker patch Some structures from the...

Ngày tải lên: 07/03/2014, 17:20

... 1A) and the DQF-COSY spectra (not shown) collected under identical conditions (Table 3) The unique spin systems His8, Lys10, Arg11 and Ala29, and the pairs of Phe and Pro residues and Gly28 and ... gradients for each structure The rmsd values and the distance and dihedral angle violations for the best 10 out of 60 structures are given in Table The final structures shown in Figs and were determined ... hydrophobic palmitoylated Cys and Phe residues and on the charged Lys and Arg residues at positions 10 and 11, which probably results in slightly different N-terminal structures for the SP-C variants...

Ngày tải lên: 16/03/2014, 16:20

... Leu8, His16, and Gly17, is present in seven structures, and another antiparallel b-bulge (B2), composed of Val57, Glu87, and Arg88, is observed for all the structures The secondary structure elements ... DNA and the b-ribbon arms, and variable contacts between additional DNA and the body of the protein [19] In the case of MC1ÆDNA complexes, we know that the protein covers at least 15 bp and that ... 1A,B) The secondary structure elements, namely an a-helix, a1 (25– 32), and five b-strands, b1 (4–9), b2 (15–21), b3 (43– 48), b4 (55–65), and b5 (79–90), are all antiparallel and packed with each...

Ngày tải lên: 22/03/2014, 17:20

... b-strands are numbered and the b5 and b7 strands are shown in red and blue, respectively G104 (equivalent to K137 of human HSP22) and R108 (equivalent to K141 of human HSP22) are shown in purple and ... indicate that this protein contains very small quantities of a-helices and is enriched in unordered structure and b-strands The residues of HSP22 that are predicted to form b-strands are indicated ... Previously, we compared the structure and properties of the wild-type HSP22 and its K141E mutant [29] The present study analyses the structure and properties of K137E and the K137,141E mutant of...

Ngày tải lên: 23/03/2014, 07:20