... 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...
... 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 Structureand expression...
... Bioinformatics and cheminformatics in drugdiscovery The combination of random screening and rational drug design have played an important role in drugdiscovery [44] The traditional drugdiscovery ... targets anddrug of the approved, clinical trial, and experimental drugs These database lead to a better understanding of the disease and benefit for drugdiscovery Src promotes tumour invasion and ... http://scop.mrc-lmb.cam.ac.uk/scop/ PDB proteinProtein Data Bank http://www.rcsb.org/pdb/home/home.d acids, and Complex MMDB Structures of proteins, nucleic o Proteinstructure at NCBI http://www.ncbi.nlm.nih.gov /Structure/ ...
... implant testing anddrugdiscovery 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 drugdiscovery 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,...
... 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 ... residues, and provided evidence that these novel proteinprotein interaction core modules play a pivotal role in regulating dendrite growth and branching of cerebellar granule cells and hippocampal ... study revealed the structural and functional determinants of the proteinprotein interaction between v-KIND and MAP2 (i.e the MAP2-binding core module in v-KIND and the v-KIND-binding core module...
... 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 ... characterized, and all were helical, monomeric and stable NOESY, 15N-1H HSQC and 13C-1H HSQC NMR spectra indicated that four of the five proteins had well-ordered and persistent main-chain and sidechain structure ... Regan lab has studied the structure, function, stability and folding of the four-helix bundle protein rop Rop is an excellent model system for understanding proteinstructureand stability: it can...
... hindrance between peptide and protein, and to relax the hydrogen added to the protein, the peptide andprotein 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,...
... 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...
... 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...
... 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...
... 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...
... 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 structureand b-strands The residues of HSP22 that are predicted to form b-strands are indicated ... Previously, we compared the structureand properties of the wild-type HSP22 and its K141E mutant [29] The present study analyses the structureand properties of K137E and the K137,141E mutant of...
... calmodulin (1PRW.pdb) and NSCP (solution structure) : )111 and )116, respectively Sequence and structural comparison between calmodulin and three different compact EF-hand proteins (NSCP, Botrychium ... Trp, Leu and Ile residues is 25 in calmodulin and 38, 37, and 35 in NSCP, B lanceolatum SCP and S erythraea calcium-binding protein, respectively Therefore, the collapse of the two EF-hand halves, ... FEBS Table Statistics of the interhelix angles within EF-hand motifs in NSCP, related EF-hand proteins and calmodulin An asterisk marks EF-hand motif that had lost Ca2+-binding capacity Helix pair...
... peptides and proteins [13], such as acidic and basic proline-rich proteins (PRP) and histatins, allowed recognizing in the presecretory salivary fragmentation pathway the action of a furinlike pro -protein ... diagnostic impact of cathepsins B, L and H from human tissues extracts (normal and tumor tissue) and extracellular uids (such as plasma and urine) and a1-proteinase inhibitor (PI) in pathogenesis ... 157 Abstracts elastase and trypsin- and chymotripsin-like proteinases) As proteinases from king red crab hepatopancreas have high enzymesubstrate afnity to Icelandic scallop proteins, a high degree...
... Asn12 and Lys17 (region 2) and between Lys34 and Asp39 (PAF) and Lys31 and Asp36 (AFP) (region 3) Two conserved GlyLys motifs are repeated in the structure, the glycines (i.e Gly5 from b1 and Gly20 ... indicate b-strands FEBS Journal 276 (2009) 2875–2890 ª 2009 The Authors Journal compilation ª 2009 FEBS 2877 Structureand dynamics of an antifungal protein G Batta et al b-strand secondary structure ... adjacent Lys9 and Lys39 Similarly, Asp23 stabilizes the juxtaposed Lys15 and Lys17 side chains The hydrophobic strand b4 is located between Cys43 and Asp46 and, as a central strand of sheet 2,...
... Two protein structures (A) and (B) are shown schematically Two pairs of positions (i, j) in (A) and m, n in (B) are selected Both structures are centered on the origin of a grid (C) at i and m and ... self-consistent 26 Taylor Fig Two protein structures (A) and (B) are shown schematically A pair of positions (i in (A) and m in B) is selected Both structures are centered on i and m and orientated by a local ... in protein structures: a procedure involving comparison of properties and relationship through simulated annealing and dynamic programming J Mol Biol 212, 403–428 Holm, L and Sander, C (1993) Protein- structure...
... Fragment-Based DrugDiscovery 115 Michael Hennig, Armin Ruf, and Walter Huber Targeting ProteinProtein Interactions and Fragment-Based DrugDiscovery ... (2009) Ligand efficiency and fragment-based drugdiscoveryDrug Discov Today 14:278–283 83 Orita M, Ohno K, Niimi T (2009) Two ‘golden ratio’ indices in fragment-based drugdiscoveryDrug Discov ... fruit in drugdiscovery at protein- protein interfaces Nature 450:1001–1009 Hajduk PJ, Greer J (2007) A decade of fragment-based drug design: strategic advances and lessons learned Nat Rev Drug Discov...
... of protein structures could lead to both deep and general or broad insights about aspects such as the folding, evolution, and function of proteins, the nature of protein ligand andproteinprotein ... of protein secondary and tertiary structures, protein docking with small molecules and with macromolecules (i.e., DNA, RNA, and proteins), simulation of dynamic behaviors of proteins, proteinstructure ... of proteinstructure comparison and applications, and computational approaches for aligning two protein structures Applications of the structurestructure alignment algorithms to protein structure...
... drugdiscoveryand development DrugDiscovery Today 11: 806-811 [14] Lowe JA, Jones P, Wilson DM (2010) Network biology as a new approach to drugdiscovery Current Opinion in DrugDiscoveryand ... These and many other such studies describe the way of incorporation of safety aspect in drugdiscovery process for Ayurvedic drugs Concept of Drug rediscovery” Contemporary Drugdiscoveryand ... extension of Drug rediscovery from ayurvedic drugs can be done for benefit of contemporary science of medicine and that would be “stage drugdiscovery based on 16 DrugDiscoveryand Development...
... AtSUN1 and AtSUN2 firmly establish that these proteins reside in the NE like their animal and fungal counterparts [17-19] SUN-Domain Proteins and Meiotic Chromosome Behavior Some animal and fungal ... SUN-domain protein structures (Figure 3A) are also shown for comparison The SUN-domain proteins of human, mouse, worm, and fission yeast differ in size and number of transmembrane and coiled-coil ... SUN-domain proteins, as represented by the founding members ZmSUN3, ZmSUN4, and ZmSUN5 A summary of the five maize SUN-domain protein genes is provided in Table and the properties and motifs...