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Showing 1 to 20 of 232 for “"substrate binding"”.
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Structure-Substrate Binding Relationships of HIV-1 Reverse Transcriptase
… 5, 486-489] were employed to study the structure-substrate binding relationships of HIV-1 RT. The activity assays of RNA-dependent DNA synthesis on both poly(rA)(dT) and a random base RNA template hybridized with a DNA oligomer showed that p51 significantly affects the enzyme activity. The …
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Insights into the Substrate Binding Specificity of Quorum-Quenching Acylase PVDQ
… chain lengths and substituents. However, the substrate binding specificity determinants of PvdQ with different bacterial ligands remain unknown and unintuitive. Elucidation of these determinants can lead to mutants with efficiency and broader substrate promiscuity. To investigate this …
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Investigating the substrate binding mechanism of the mitochondrial ADP/ATP carrier
… a matrix gate. However, the molecular nature of substrate binding remains unresolved. Substrate binding is concomitant with the structural movements required for translocation, because substrate binding and release provides the free energy changes for the disruption and formation of the gates. …
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Catalysis, substrate binding and specificity in the amidase from Nesterenkonia species
… of NitN specificity on short aliphatic amide substrates by analyzing binding and interactions of these molecules with the NitN binding pocket. To probe the catalytic role of the two active site glutamate residues (Glu61 and Glu139) using NitN as a model enzyme. To monitor the activity, …
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Analysis of The Biochemical and Cellular Activities of Substrate Binding By The Molecular Chaperone Hsp110/Sse1
… by cycling through high and low affinity binding of unfolded protein clients to facilitate folding. The Hsp110 class of chaperones are divergent relatives of Hsp70 that are extremely effective in preventing protein aggregation but lack the hallmark folding activity seen in Hsp70s. Hsp110s …
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Deciphering Functional Significance of Substrate-Binding Domain of Ssa1 on Heat-Shock Response and Prion Propagation
… Hsp70 is comprised of two domains: nucleotide-binding domain (NBD) and substrate-binding domain (SBD). In this work, a well-established yeast system and a combination of computational biology, genetics, structural biology, biochemistry and molecular biology were utilized to decipher the role of …
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Substrate binding to MshB, a zinc-dependent deacetylase in the mycothiol biosynthetic pathway of Mycobacterium tuberculosis
… regarding important residues involved in substrate binding and the catalytic mechanism. The findings presented here provide some insight into the substrate binding mechanism and support a recent publication that infers that Tyr-142 plays an important role in the catalytic mechanism, as …
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Elucidating the role of membranes in modulating the thermodynamics and kinetics of substrate binding to Thromboxane Synthase
Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2013-04-26T15:02:42Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Varma, Snehita.pdf: 1462422 bytes, checksum: 951f441072241284d93adc7f4f9fd9a0 (MD5)
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Biophysical Characterization of the Interaction between the Universal Stress G4LZI3 protein and Schistosoma mansoni Hsp60 Substrate Binding Domain
… insight on the structure of both proteins, their binding sites and affinities as well as in the discovery of a potential inhibitor, Epolactaene with a potential of breaking the interaction between the two proteins. Molecular dynamic simulations were implemented in the present study chosen based on …
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The role of the N domain in substrate binding, oligomerization, and allosteric regulation of the AAA+ Lon protease
… which convert the chemical energy of ATP binding and hydrolysis into mechanical work to unfold and translocate substrates into an internal degradation chamber. Substrates are targeted to AAA+ proteases by degradation tags (degrons). In E. coli, the Lon protease is responsible for the …
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Biophysical investigations of the interaction between substrate binding domain of Hsp40 and the RING finger domain of Retinoblastoma Binding Protein 6
… the RING finger domain of the Retinoblastoma binding protein 6 (RBBP6) and the substrate binding domain of heat shock protein 40 (SBDHsp40) suggested a putative interaction between these two proteins. In this study molecular dynamic simulations were used to confirm the interaction between the …
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The Invariant Arginine In Motif 2 of ESCHERICHIA COLI Alanyl-tRNA Synthetase : Is Important For Catalysis But Not For Substrate Binding
<p>Structural motifs 2 and 3, located in the active site of class II aminoacyl-tRNA synthetases, each contain an invariant arginine thought to participate in interactions with ATP. For <em>Escherichia coli</em> alanyl-tRNA synthetase (AlaRS), sequence comparisons indicate that Arg69 should be …
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The role of outer-sphere residues and substrate-binding at the 3-mercaptopropionic acid dioxygenase (3mdo) active site: a combined spectroscopic and computational investigation
… L-cysteine to cysteine sulfinic acid with high substrate-specificity. Unlike CDO, bacterial 3-mercaptopropionate dioxygenase from Azotobacter vinelandii (Av3MDO) is a promiscuous TDO that oxidizes a variety of thiol substrates. Given both enzymes show similar active site geometries, the drastic …
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Biochemical Studies of Ribonuclease P of Tetrahymena Thermophila
… experiments with a photoaffinity-labeled substrate have been performed with the RNase P RNA subunit and holoenzymes from various sources. Experimental studies clearly reveal that the prokaryotic RNA subunit is involved in substrate binding, but that the eukaryotic RNA subunit alone is …
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Studies to Characterize the Requirements for the Binding and Release of ERdj3, a Mammalian ER DnaJ Homolog, from Substrates
… that ERdj3 binds directly to two unfolded substrates: immunoglobulin γHC and denatured firefly luciferase. Using mutagenesis studies on ERdj3 in both <em>in vivo</em> and <em>in vitro</em> binding assays, we defined ERdj3’s critical amino acids in domain I that contribute to substrate …
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Structural studies of the YedU stress protein
… composed of Cys184, His185, and Asp213. A metal-binding site was identified, where a zinc(II) ion is coordinated by a 2-His-1-carboxylate motif composed of His85, Glu90, and His122. The possible functions of the metal-binding site and the Cys184-His185-Asp213 triad are discussed. \r\nIt was …
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Investigating the functionality of the transmembranes in GusB by fusing it with LacY using the polymerase chain reaction.
… with two other structural genes. However, the substrate binding sites of GusB are not currently known and therefore this research project was focused on fusing GusB with a different well-studied secondary transporter known as lactose ‘permease’ (LacY). LacY is a protein which facilitates the …
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Structure and Mechanism of a Eukaryotic FMN Adenylyltransferase
… have suggested that the architectures of the substrate binding and catalytic sites are different. Sequence comparison reveals that eukaryotic FMNAT is related to the PAPS reductase-like family, which belongs to the adenine nucleotide α hydrolase-like superfamily. Despite the classification of …
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