The Key Residues of Active Sites on the Catalytic Fragment for Paclitaxel Interacting with Poly (ADP-Ribose) Polymerase

Protein kinase C-δ (PKC-δ) is an important protein in the immune system of higher vertebrates. Lampreys, as the most primitive vertebrates, have a uniquevariable lymphocyte receptor (VLR) immune system. PKC-δ-like is a crucial functional gene in lampreys and is highly expressed in their immune organs. In this study, lampreys were stimulated with different immunogens, and lipopolysaccharide (LPS) was found to increase the expression of PKC-δ-like. Overexpression of PKC-δ-like could also effectively activate the innate immune response. We further demonstrated that PKC-δ-like-CF, a catalytic fragment of PKC-δ-like, is responsible for activating the innate immune response, and Thr-211, which is Thr-419 of PKC-δ-like, was confirmed to be the key site affecting PKC-δ-like-CF activity. These results indicated that PKC-δ-like from lamprey may have an important role in the innate immune response.

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Photochemical mapping of the active site of myosin

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.1992.0044 ◽

1992 ◽

Vol 336 (1276) ◽

pp. 55-61 ◽

Cited By ~ 24

Keyword(s):

Active Site ◽

Metal Ion ◽

Active Sites ◽

Cross Linking ◽

Detailed Structure ◽

Atp Binding Site ◽

Adenine Ring ◽

Skeletal Myosin ◽

Key Residues ◽

Specific Labelling

The active sites of myosin from skeletal, smooth and scallop muscle have been partly characterized by use of a series of photoreactive analogues of ATP. Specific labelling was attained by trapping these analogues in their diphosphate forms at the active sites by either cross-linking two reactive thiols (skeletal myosin) or by formation of stable vanadate-metal ion transition state-like complexes (smooth muscle and scallop myosin). By use of this approach combined with appropriate chemistry, several key residues in all three myosins have been identified which bind at or near the adenine ring, the ribose ring and to the γ-phosphate of ATP. This information should aid in the solution of the crystal structure of the heads of myosin and in defining a detailed structure of the ATP binding site.

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Computational Investigation of Bisphosphate Inhibitors of 3-Deoxy-d-manno-octulosonate 8-phosphate Synthase

Molecules ◽

10.3390/molecules24132370 ◽

2019 ◽

Vol 24 (13) ◽

pp. 2370 ◽

Cited By ~ 3

Author(s):

Jéssica de Oliveira Araújo ◽

Alberto Monteiro dos Santos ◽

Jerônimo Lameira ◽

Cláudio Nahum Alves ◽

Anderson Henrique Lima

Keyword(s):

Active Sites ◽

Antimicrobial Agents ◽

Md Simulations ◽

Hydroxyl Groups ◽

Ligand Complex ◽

Effective Interactions ◽

Key Enzyme ◽

The Many ◽

Key Residues ◽

Computational Molecular Modeling

The synthase, 3-deoxy-d-manno-octulosonate 8-phosphate (KDO8P), is a key enzyme for the lipopolysaccharide (LPS) biosynthesis of gram-negative bacteria and a potential target for developing new antimicrobial agents. In this study, computational molecular modeling methods were used to determine the complete structure of the KDO8P synthase from Neisseria meningitidis and to investigate the molecular mechanism of its inhibition by three bisphosphate inhibitors: BPH1, BPH2, and BPH3. Our results showed that BPH1 presented a protein–ligand complex with the highest affinity, which is in agreement with experimental data. Furthermore, molecular dynamics (MD) simulations showed that BPH1 is more active due to the many effective interactions, most of which are derived from its phosphoenolpyruvate moiety. Conversely, BPH2 exhibited few hydrogen interactions during the MD simulations with key residues located at the active sites of the KDO8P synthase. In addition, we hydroxylated BPH2 to create the hypothetical molecule named BPH3, to investigate the influence of the hydroxyl groups on the affinity of the bisphosphate inhibitors toward the KDO8P synthase. Overall, we discuss the main interactions between the KDO8P synthase and the bisphosphate inhibitors that are potential starting points for the design of new molecules with significant antibiotic activities.

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In-silico investigation of umami peptides with receptor T1R1/T1R3 for the discovering potential targets: A combined modeling approach

10.1101/2021.10.10.463792 ◽

2021 ◽

Author(s):

Wenli Wang ◽

Zhiyong Cui ◽

Menghua Ning ◽

Tianxing Zhou ◽

Yuan Liu

Keyword(s):

Amino Acids ◽

Molecular Docking ◽

Sequence Analysis ◽

In Silico ◽

Quantum Chemical ◽

Active Sites ◽

Food Industry ◽

Time Saving ◽

Animal Growth ◽

Key Residues

Umami, providing amino acids/peptides for animal growth, represents one of the major attractive taste modalities. The biochemical and umami properties of peptide are both important for scientific research and food industry. In this study, we did the sequence analysis of 205 umami peptides with 2-18 amino acids, sought the active sites of umami peptides by quantum chemical simulations and investigated their recognition residues with receptor T1R1/T1R3 by molecular docking. The results showed the peptides with 2-3 amino acids accounting for 44% of the total umami peptides. Residues D and E are the key active sites no matter where they in peptides (N-terminal, C-terminal or middle), when umami peptides contain D/E residues. N69, D147, R151, A170, S172, S276 and R277 residues in T1R1 receptor were deem to the key residues binding umami peptides. Finally, a powerful decision rule for umami peptides was proposed to predict potential umami peptides, which was convenient, time saving and efficiently.

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Structure of Allium lachrymatory factor synthase elucidates catalysis on sulfenic acid substrate

10.1101/142687 ◽

2017 ◽

Cited By ~ 1

Author(s):

Takatoshi Arakawa ◽

Yuta Sato ◽

Jumpei Takabe ◽

Noriya Masamura ◽

Masahiro Kato ◽

...

Keyword(s):

Crystal Structures ◽

Active Site ◽

Active Sites ◽

Catalytic Mechanism ◽

Sigmatropic Rearrangement ◽

Natural Production ◽

Lachrymatory Factor ◽

Biological Decomposition ◽

Key Residues ◽

Lachrymatory Factor Synthase

AbstractNatural lachrymatory effects are invoked by small volatile S-oxide compounds. They are produced through alkene sulfenic acids by the action of lachrymatory factor synthase (LFS). Here we present the crystal structures of onion LFS (AcLFS) revealed in solute-free and two solute-stabilized forms. Each structure adopts a single seven-stranded helix-grip fold possessing an internal pocket. Mutagenesis analysis localized the active site to a layer near the bottom of the pocket, which is adjacent to the deduced key residues Arg71, Glu88, and Tyr114. Solute molecules visible on the active site have suggested that AcLFS accepts various small alcohol compounds as well as its natural substrate, and they inhibit this substrate according to their chemistry. Structural homologs have been found in the SRPBCC superfamily, and comparison of the active sites has demonstrated that the electrostatic potential unique to AcLFS could work in capturing the substrate in its specific state. Finally, we propose a rational catalytic mechanism based on intramolecular proton shuttling in which the microenvironment of AcLFS can bypass the canonical [1,4]-sigmatropic rearrangement principle established by microwave studies. Beyond revealing how AcLFS generates the lachrymatory compound, this study provides insights into the molecular machinery dealing with highly labile organosulfur species.Significance statementCrushing of onion liberates a volatile compound, syn-propanethial S-oxide (PTSO), which causes lachrymatory effect on humans. We present the crystal structures of onion LFS (AcLFS), the enzyme responsible for natural production of PTSO. AcLFS features a barrel-like fold, and mutagenic and inhibitory analyses revealed that the key residues are present in the central pocket, harboring highly concentrated aromatic residues plus a dyad motif. The architecture of AcLFS is widespread among proteins with various biological functions, such as abscisic acid receptors and polyketide cyclases, and comparisons with these homologs indicate that unique steric and electronic properties maintain the pocket as a reaction compartment. We propose the molecular mechanism behind PTSO generation and shed light on biological decomposition of short-lived sulfur species.

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mRNA Interferase Bacillus cereus BC0266 Shows MazF-Like Characteristics Through Structural and Functional Study

Toxins ◽

10.3390/toxins12060380 ◽

2020 ◽

Vol 12 (6) ◽

pp. 380

Author(s):

Sung-Min Kang ◽

Ji Sung Koo ◽

Chang-Min Kim ◽

Do-Hee Kim ◽

Bong-Jin Lee

Keyword(s):

Bacillus Cereus ◽

Active Sites ◽

Cellular Growth ◽

Functional Study ◽

Independent Manner ◽

Vitro Assay ◽

High Resolution Structure ◽

Response To Stress ◽

Key Residues

Toxin–antitoxin (TA) systems are prevalent in bacteria and are known to regulate cellular growth in response to stress. As various functions related to TA systems have been revealed, the importance of TA systems are rapidly emerging. Here, we present the crystal structure of putative mRNA interferase BC0266 and report it as a type II toxin MazF. The MazF toxin is a ribonuclease activated upon and during stressful conditions, in which it cleaves mRNA in a sequence-specific, ribosome-independent manner. Its prolonged activity causes toxic consequences to the bacteria which, in turn, may lead to bacterial death. In this study, we conducted structural and functional investigations of Bacillus cereus MazF and present the first toxin structure in the TA system of B. cereus. Specifically, B. cereus MazF adopts a PemK-like fold and also has an RNA substrate-recognizing loop, which is clearly observed in the high-resolution structure. Key residues of B. cereus MazF involved in the catalytic activity are also proposed, and in vitro assay together with mutational studies affirm the ribonucleic activity and the active sites essential for its cellular toxicity.

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Structure and allosteric regulation of human IDH3 holoenzyme

10.1101/2020.06.25.170399 ◽

2020 ◽

Author(s):

Pengkai Sun ◽

Yan Liu ◽

Tengfei Ma ◽

Jianping Ding

Keyword(s):

Active Sites ◽

Critical Role ◽

Allosteric Regulation ◽

Kinetic Studies ◽

Tca Cycle ◽

Allosteric Site ◽

Functional Roles ◽

The Tca Cycle ◽

And Function ◽

Key Residues

AbstractHuman NAD-dependent isocitrate dehydrogenase or IDH3 catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the TCA cycle. We here report the structure of the IDH3 holoenzyme, in which the αβ and αγ heterodimers assemble the α2βγ heterotetramer via their clasp domains, and two α2βγ heterotetramers assemble the (α2βγ)2 heterooctamer via the β and γ subunits. The functional roles of the key residues involved in the assembly and allosteric regulation are validated by mutagenesis and kinetic studies. The allosteric site plays an important role but the pseudo allosteric site plays no role in the allosteric activation; the activation signal from the allosteric site is transmitted to the active sites of both heterodimers via the clasp domains; and the N-terminus of the γ subunit plays a critical role in the formation and function of the holoenzyme. These findings reveal the molecular mechanism of the assembly and allosteric regulation of human IDH3 holoenzyme.

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Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors

Biochemical Journal ◽

10.1042/bj20070970 ◽

2007 ◽

Vol 408 (2) ◽

pp. 193-201 ◽

Cited By ~ 73

Author(s):

Huanchen Wang ◽

Ming-Sheng Peng ◽

Yi Chen ◽

Jie Geng ◽

Howard Robinson ◽

...

Keyword(s):

Side Effects ◽

Active Sites ◽

Structural Information ◽

Inflammatory Diseases ◽

Structural Basis ◽

Pde4 Inhibitor ◽

Selective Inhibitors ◽

Phosphodiesterase 4 ◽

Catalytic Domains ◽

Key Residues

PDE4 (phosphodiesterase-4)-selective inhibitors have attracted much attention as potential therapeutics for the treatment of both depression and major inflammatory diseases, but their practical application has been compromised by side effects. A possible cause for the side effects is that current PDE4-selective inhibitors similarly inhibit isoforms from all four PDE4 subfamilies. The development of PDE4 subfamily-selective inhibitors has been hampered by a lack of structural information. In the present study, we rectify this by providing the crystal structures of the catalytic domains of PDE4A, PDE4B and PDE4D in complex with the PDE4 inhibitor NVP {4-[8-(3-nitrophenyl)-[1,7]naphthyridin-6-yl]benzoic acid} as well as the unliganded PDE4C structure. NVP binds in the same conformation to the deep cAMP substrate pocket and interacts with the same residues in each instance. However, detailed structural comparison reveals significant conformational differences. Although the active sites of PDE4B and PDE4D are mostly comparable, PDE4A shows significant displacements of the residues next to the invariant glutamine residue that is critical for substrate and inhibitor binding. PDE4C appears to be more distal from other PDE4 subfamilies, with certain key residues being disordered. Our analyses provide the first structural basis for the development of PDE4 subfamily-selective inhibitors.

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Site-selective 1H/2H labeling enables artifact-free 1H CPMG relaxation dispersion experiments in aromatic side chains

Journal of Biomolecular NMR ◽

10.1007/s10858-019-00275-z ◽

2019 ◽

Vol 73 (10-11) ◽

pp. 633-639

Author(s):

Heiner N. Raum ◽

Julia Schörghuber ◽

Matthias Dreydoppel ◽

Roman J. Lichtenecker ◽

Ulrich Weininger

Keyword(s):

Active Sites ◽

Relaxation Dispersion ◽

Side Chains ◽

Anomalous Relaxation ◽

Cpmg Relaxation Dispersion ◽

Key Residues ◽

Site Selective ◽

Unfolding Kinetics ◽

Kinetics Of ◽

Aromatic Side Chains

Abstract Aromatic side chains are often key residues in enzyme active sites and protein binding sites, making them attractive probes of protein dynamics on the millisecond timescale. Such dynamic processes can be studied by aromatic 13C or 1H CPMG relaxation dispersion experiments. Aromatic 1H CPMG relaxation dispersion experiments in phenylalanine, tyrosine and the six-ring moiety of tryptophan, however, are affected by 3J 1H–1H couplings which are causing anomalous relaxation dispersion profiles. Here we show that this problem can be addressed by site-selective 1H/2H labeling of the aromatic side chains and that artifact-free relaxation dispersion profiles can be acquired. The method has been further validated by measuring folding–unfolding kinetics of the small protein GB1. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. Furthermore, the CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained directly from the spectra. In summary, site-selective 1H/2H labeling enables artifact-free aromatic 1H CPMG relaxation dispersion experiments in phenylalanine and the six-ring moiety of tryptophan, thereby extending the available methods for studying millisecond dynamics in aromatic protein side chains.

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HOMOLOGY MODELING AND SUBSTRATE BINDING STUDY OF HUMAN KYNURENINE AMINOTRANSFERASE III

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633612500587 ◽

2012 ◽

Vol 11 (04) ◽

pp. 855-870 ◽

Cited By ~ 4

Author(s):

YU XU ◽

QING-CHUAN ZHENG ◽

HONG-XING ZHANG ◽

CHIA-CHUNG SUN

Keyword(s):

Homology Modeling ◽

Active Sites ◽

Md Simulation ◽

3D Structure ◽

Strong Interactions ◽

Binding Modes ◽

Kynurenine Aminotransferase ◽

Dynamics Simulations ◽

Key Residues ◽

Good Agreement

Kynurenine aminotransferase III (KAT III) is a novel member of the kynurenine aminotransferase enzyme family. Its active site topology and structure characteristics have not been established. In this study, with extensive computational simulations, including homology modeling and molecular dynamics simulations, a 3D structure model of human KAT III dimer was created and refined. Furthermore, CDOCKER approach was employed to dock two ligands (L-methionine and L-tryptophan) into the active sites of human KAT III dimer and uncover the ligand-binding modes. The complexes were subjected to 5 ns MD simulation, and the results indicate that TYR119 and TRP13 might be the key residues as they have the large contributions to the binding affinity, which is in good agreement with the experimental results. Moreover, another two residues (ASP120 and TYR57) are also found that their strong interactions stabilize the whole system. The structural and biochemical insights obtained from the present study will be helpful for designing the specific inhibitors of human KAT III.

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