Investigation of the Detailed AMPylated Reaction Mechanism for the Huntingtin Yeast-Interacting Protein E Enzyme HYPE

AMPylation is a prevalent posttranslational modification that involves the addition of adenosine monophosphate (AMP) to proteins. Exactly how Huntingtin-associated yeast-interacting protein E (HYPE), as the first human protein, is involved in the transformation of the AMP moiety to its substrate target protein (the endoplasmic reticulum chaperone binding to immunoglobulin protein (BiP)) is still an open question. Additionally, a conserved glutamine plays a vital key role in the AMPylation reaction in most filamentation processes induced by the cAMP (Fic) protein. In the present work, the detailed catalytic AMPylation mechanisms in HYPE were determined based on the density functional theory (DFT) method. Molecular dynamics (MD) simulations were further used to investigate the exact role of the inhibitory glutamate. The metal center, Mg2+, in HYPE has been examined in various coordination configurations, including 4-coordrinated, 5-coordinated and 6-coordinated. DFT calculations revealed that the transformation of the AMP moiety of HYPE with BiP followed a sequential pathway. The model with a 4-coordinated metal center had a barrier of 14.7 kcal/mol, which was consistent with the experimental value and lower than the 38.7 kcal/mol barrier of the model with a 6-coordinated metal center and the 31.1 kcal/mol barrier of the model with a 5-coordinated metal center. Furthermore, DFT results indicated that Thr518 residue oxygen directly attacks the phosphorus, while the His363 residue acts as H-bond acceptor. At the same time, an MD study indicated that Glu234 played an inhibitory role in the α-inhibition helix by regulating the hydrogen bond interaction between Arg374 and the Pγ of the ATP molecule. The revealed sequential pathway and the inhibitory role of Glu234 in HYPE were inspirational for understanding the catalytic and inhibitory mechanisms of Fic-mediated AMP transfer, paving the way for further studies on the physiological role of Fic enzymes.

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Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

10.26434/chemrxiv.9209180 ◽

2019 ◽

Author(s):

Bella Grigorenko ◽

Igor Polyakov ◽

Alexander Nemukhin

Keyword(s):

Adenylyl Cyclase ◽

Bond Cleavage ◽

Cyclic Adenosine Monophosphate ◽

Adenosine Monophosphate ◽

Md Simulations ◽

Coordination Shell ◽

Energy Profile ◽

One Step ◽

Type V

We report a mechanism of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V adenylyl cyclase revealed in molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of computationally derived enzyme-substrate (ES) structures showing an important role of coordination shells of magnesium ions in the solvent accessible active site. Several stable six-fold coordination shells of MgA2+ are observed in MD simulations of ES complexes. In the lowest energy ES conformation, the coordination shell of MgA2+ does not include the Oδ1 atom of the conserved Asp440 residue. Starting from this conformation, a one-step reaction mechanism is characterized which includes proton transfer from the ribose O3'H3' group in ATP to Asp440 via a shuttling water molecule and PA-O3A bond cleavage and O3'-PA bond formation. The energy profile of this route is consistent with the observed reaction kinetics. In a higher energy ES conformation, MgA2+ is bound to the Oδ1(Asp440) atom as suggested in the relevant crystal structure of the protein with a substrate analog. The computed energy profile initiated by this ES is characterized by higher energy expenses to complete the reaction. Consistently with experimental data, we show that the Asp440Ala mutant of the enzyme should exhibit a reduced but retained activity. All considered reaction pathways include proton wires from the O3'H3' group via shuttling water molecules.

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Mechanistic insight into the selective trans-1,4-polymerization of butadiene by terpyridine–iron(II) complexes — A computational study

Canadian Journal of Chemistry ◽

10.1139/v09-101 ◽

2009 ◽

Vol 87 (10) ◽

pp. 1392-1405 ◽

Cited By ~ 17

Author(s):

Sven Tobisch

Keyword(s):

Density Functional ◽

Computational Study ◽

Dft Method ◽

Chain Growth ◽

Functional Theory ◽

The Density Functional Theory ◽

Insertion Mechanism ◽

Trans Regulation ◽

Insight Into

The density functional theory (DFT) method has been employed to unravel mechanistic intricacies of the 1,4-polymerization of 1,3-butadiene mediated by the [(η3-RC3H4)FeII(C15H11N3)(η2-C4H6)]+ terpyridine–iron(II) active catalyst species. The π-allyl-insertion mechanism is operative for chain growth, whilst the alternative σ-allyl-insertion mechanism has been explicitly demonstrated as being inoperable. This study elucidates the mechanism of cis–trans regulation and unveils the factors that govern the observed high trans-1,4 stereoselectivity, in particular, the discriminative role of allylic isomerization. An atactic trans-1,4-polydiene is expected from polymerization of a terminally monosubstituted butadiene, the experimental results of which have not been reported thus far.

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Density Functional Theory (DFT) and Natural Bond Orbital (NBO) Investigation of Intra/Intermolecular Hydrogen Bond Interaction in Sulfonated Nata-De Coco-Water (NDCS-(H2O)n)

Journal of Computational and Theoretical Nanoscience ◽

10.1166/jctn.2020.8945 ◽

2020 ◽

Vol 17 (6) ◽

pp. 2812-2819

Author(s):

Sitti Rahmawati ◽

Cynthia Linaya Radiman ◽

Muhamad Abdulkadir Martoprawiro ◽

Siti Nuryanti

Keyword(s):

Hydrogen Bonds ◽

Proton Transfer ◽

Density Functional ◽

Intermolecular Hydrogen Bond ◽

Lone Pair ◽

Dft Method ◽

Nbo Analysis ◽

Hydrogen Bond Interaction ◽

Sulfonic Group ◽

The One

This research aim to study the conformation, hydrogen bonding network, and stability of all possible molecular interactions between sulfonated nata-de-coco membranes with water (NDCS-(H2O)n), n = 1–5) as well as associate them with results of phosphorylated nata-de-coco reported previously, to determine the potential of proton transfer within both systems. The calculations used DFT method at the B3LYP/6-311G** level as well as NBO analysis. The strongest hydrogen bonds were found among sulfonic group in NDCS-(H2O)5 and the oxygen in the water molecules. The stabilization energy of NDCS-(H2O)5 is 98.9 kcal/mol, That is much greater than that found in NDCP-(H2O)5 This suggests that the NDCS was more easily to donate its lone pair and that the hydrogen bonds between sulfonic group and water molecule were stronger, so that it was easier to transfer protons to another sulfonic group than to NDCP. The energy profile showed that barrier energy was roughly 58.1 kcal/mol and 138.6 kcal/mol for NDCS-(H2O)5 and NDCP-(H2O)5 respectively. Proton transfer in NDCS-(H2O)5 generated a lower energy-barrier than the one in NDCP-(H2O)5

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Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study

10.26434/chemrxiv.13567349 ◽

2021 ◽

Author(s):

Aashish Bhatt ◽

Md. Ehesan Ali

Keyword(s):

Hydrogen Bonding ◽

In Silico ◽

Density Functional ◽

Experimental Studies ◽

Salt Bridge ◽

Md Simulations ◽

Enzymatic Activities ◽

Wild Type ◽

Long Distance

<div>Human cystathionine β-synthase (hCBS) is a unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyses the condensation reactions in the transsulfuration pathways. The specific role of Heme in the enzymatic activities has not yet been established, however, several experimental studies indicated the bi-directional communications between the Heme and PLP. Performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme, we have investigated In Silico dynamical aspects of the bi-directional communications. Furthermore, we have investigated the comparative aspects of electron density overlap across the communicating pathways adopting the density functional theory (DFT) in conjunction with the hybrid exchange correlation functional for the CSBWT (wild-type) and CBSR266K (mutated) case. The atomistic dynamical simulations and subsequent explorations of the electronic structure not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control the such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns as well as salt-bridge interactions play the pivotal role in such long distant bi-directional communications.</div>

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The Inhibitory Role of B7-H4 in Antitumor Immunity: Association with Cancer Progression and Survival

Clinical and Developmental Immunology ◽

10.1155/2011/695834 ◽

2011 ◽

Vol 2011 ◽

pp. 1-8 ◽

Cited By ~ 32

Author(s):

Changjun He ◽

Haiquan Qiao ◽

Hongchi Jiang ◽

Xueying Sun

Keyword(s):

Cancer Progression ◽

Antitumor Immunity ◽

Human Cancer ◽

Physiological Role ◽

T Cell Response ◽

Soluble Form ◽

Peripheral Tissues ◽

Inhibitory Role ◽

Pertinent Data

B7-H4 is one of the most recently identified members of B7 superfamily of costimulatory molecules serving as an inhibitory modulator of T-cell response. B7-H4 is broadly expressed in human peripheral tissues and inducibly expressed in immune cells. The expression of B7-H4 has been observed in various types of human cancer tissues, and its soluble form has been detected in blood samples from cancer patients. However, its precise physiological role is still elusive, as its receptor has not been identified and the expression levels are not consistent. This paper summarizes the pertinent data on the inhibitory role of B7-H4 in antitumor immunity and its association with cancer progression and survival in human patients. The paper also discusses the clinical significance of investigating B7-H4 as potential markers for cancer diagnosis and prognosis, and as therapeutic targets.

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Revealing the Role of the Calcineurin B-Like Protein-Interacting Protein Kinase 9 (CIPK9) in Rice Adaptive Responses to Salinity, Osmotic Stress, and K+ Deficiency

Plants ◽

10.3390/plants10081513 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1513

Author(s):

Sergey Shabala ◽

Mohammad Alnayef ◽

Jayakumar Bose ◽

Zhong-Hua Chen ◽

Gayatri Venkataraman ◽

...

Keyword(s):

Osmotic Stress ◽

Physiological Role ◽

Carbon Gain ◽

Adaptive Responses ◽

Interacting Protein ◽

Rice Mutant ◽

Calcineurin B ◽

K Deficiency ◽

Low K

In plants, calcineurin B-like (CBL) proteins and their interacting protein kinases (CIPK) form functional complexes that transduce downstream signals to membrane effectors assisting in their adaptation to adverse environmental conditions. This study addresses the issue of the physiological role of CIPK9 in adaptive responses to salinity, osmotic stress, and K+ deficiency in rice plants. Whole-plant physiological studies revealed that Oscipk9 rice mutant lacks a functional CIPK9 gene and displayed a mildly stronger phenotype, both under saline and osmotic stress conditions. The reported difference was attributed to the ability of Oscipk9 to maintain significantly higher stomatal conductance (thus, a greater carbon gain). Oscipk9 plants contained much less K+ in their tissues, implying the role of CIPK9 in K+ acquisition and homeostasis in rice. Oscipk9 roots also showed hypersensitivity to ROS under conditions of low K+ availability suggesting an important role of H2O2 signalling as a component of plant adaptive responses to a low-K environment. The likely mechanistic basis of above physiological responses is discussed.

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Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires

10.26434/chemrxiv.9209180.v1 ◽

2019 ◽

Author(s):

Bella Grigorenko ◽

Igor Polyakov ◽

Alexander Nemukhin

Keyword(s):

Adenylyl Cyclase ◽

Bond Cleavage ◽

Cyclic Adenosine Monophosphate ◽

Adenosine Monophosphate ◽

Md Simulations ◽

Coordination Shell ◽

Energy Profile ◽

One Step ◽

Type V

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Gonadotropin Inhibitory Hormone Down-Regulates the Brain-Pituitary Reproductive Axis of Male European Sea Bass (Dicentrarchus labrax)1

Biology of Reproduction ◽

10.1095/biolreprod.116.139022 ◽

2016 ◽

Vol 94 (6) ◽

Cited By ~ 24

Author(s):

José A. Paullada-Salmerón ◽

Mairi Cowan ◽

María Aliaga-Guerrero ◽

Francesca Morano ◽

Silvia Zanuy ◽

...

Keyword(s):

Dicentrarchus Labrax ◽

Physiological Role ◽

Sea Bass ◽

Central Administration ◽

European Sea Bass ◽

Inhibitory Role ◽

Reproductive Axis ◽

Gonadotropin Inhibitory Hormone ◽

Different Doses

Abstract Gonadotropin-inhibitory hormone (GnIH) inhibits gonadotropin synthesis and release from the pituitary of birds and mammals. However, the physiological role of orthologous GnIH peptides on the reproductive axis of fish is still uncertain, and their actions on the main neuroendocrine systems controlling reproduction (i.e., GnRHs, kisspeptins) have received little attention. In a recent study performed in the European sea bass, we cloned a cDNA encoding a precursor polypeptide that contained C-terminal MPMRFamide (sbGnIH-1) and MPQRFamide (sbGnIH-2) peptide sequences, developed a specific antiserum against sbGnIH-2, and characterized its central and pituitary GnIH projections in this species. In this study, we analyzed the effects of intracerebroventricular injection of sbGnIH-1 and sbGnIH-2 on brain and pituitary expression of reproductive hormone genes (gnrh1, gnrh2, gnrh3, kiss1, kiss2, gnih, lhbeta, fshbeta), and their receptors (gnrhr II-1a, gnrhr II-2b, kiss1r, kiss2r, and gnihr) as well as on plasma Fsh and Lh levels. In addition, we determined the effects of GnIH on pituitary somatotropin (Gh) expression. The results obtained revealed the inhibitory role of sbGnIH-2 on brain gnrh2, kiss1, kiss2, kiss1r, gnih, and gnihr transcripts and on pituitary fshbeta, lhbeta, gh, and gnrhr-II-1a expression, whereas sbGnIH-1 only down-regulated brain gnrh1 expression. However, at different doses, central administration of both sbGnIH-1 and sbGnIH-2 decreased Lh plasma levels. Our work represents the first study reporting the effects of centrally administered GnIH in fish and provides evidence of the differential actions of sbGnIH-1 and sbGnIH-2 on the reproductive axis of sea bass, the main inhibitory role being exerted by the sbGnIH-2 peptide.

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Activation of the Cyano Group at Imidazole via Copper Stimulated Alcoholysis

Inorganics ◽

10.3390/inorganics7070087 ◽

2019 ◽

Vol 7 (7) ◽

pp. 87

Author(s):

Rezeda Gayfullina ◽

Sirpa Jääskeläinen ◽

Igor O. Koshevoy ◽

Pipsa Hirva

Keyword(s):

Density Functional ◽

Cyano Group ◽

Dft Method ◽

Structural Features ◽

Metal Center ◽

Monomeric Complex ◽

Additional Ligand ◽

Alcohol Solvents ◽

Alkoxy Groups ◽

Absorption Characteristics

Reactions of 4,5-dicyano-1-methylimidazole with CuX2 (X = Cl, Br) in alcohol solvents (ethanol and methanol) resulted in the formation of Cu(II) carboximidate complexes [CuCl2(5- cyano-4-C(OEt)N-1-methylimidazole)(EtOH)] (1), [Cu2(µ-Cl)2Cl2(5-cyano-4-C(OMe)N-1-methylimidazole)2] (2), [Cu2(µ-Br)2Br2(5-cyano-4-C(OMe)N-1-methylimidazole)2] (3), and [Cu2(µ-Br)2Br2(5-cyano-4-C(OEt)N-1-methylimidazole)2] (4). The structures were determined by the X-ray crystallographic method, and further spectroscopic and computational methods were employed to explain the structural features. The solvent contributed to the alcoholysis reaction of the cyano group, as the result of which the ligand coordinated to the metal center in bidentate mode forming a five-membered chelating ring. In 1, the solvent also acts as an additional ligand, which coordinates to the metal center of a monomeric complex. In compounds 2–4, two halogen ligands link the metal atoms forming dihalo-bridged copper dimers. The infrared absorption characteristics were verified by simulation of the infrared spectra at the density functional theory level. In addition, the electronic absorption characteristics were explained by simulation of the UV–Vis spectra using the TD-DFT method. Molecular modelling at the DFT level was performed to study the effects of halogen type and steric hindrance of the alkoxy groups in forming the copper(II) complexes.

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Cannabinoid Receptor Interacting Protein 1a (CRIP1a) in Health and Disease

Biomolecules ◽

10.3390/biom10121609 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1609

Author(s):

Emily E. Oliver ◽

Erin K. Hughes ◽

Meaghan K. Puckett ◽

Rong Chen ◽

W. Todd Lowther ◽

...

Keyword(s):

Cellular Localization ◽

Cannabinoid Receptors ◽

Cannabinoid Receptor ◽

Physiological Role ◽

Interacting Protein ◽

Cancer Subtypes ◽

Health And Disease ◽

Neuronal Distribution ◽

And Function

Endocannabinoid signaling depends upon the CB1 and CB2 cannabinoid receptors, their endogenous ligands anandamide and 2-arachidonoylglycerol, and intracellular proteins that mediate responses via the C-terminal and other intracellular receptor domains. The CB1 receptor regulates and is regulated by associated G proteins predominantly of the Gi/o subtypes, β-arrestins 1 and 2, and the cannabinoid receptor-interacting protein 1a (CRIP1a). Evidence for a physiological role for CRIP1a is emerging as data regarding the cellular localization and function of CRIP1a are generated. Here we summarize the neuronal distribution and role of CRIP1a in endocannabinoid signaling, as well as discuss investigations linking CRIP1a to development, vision and hearing sensory systems, hippocampus and seizure regulation, and psychiatric disorders including schizophrenia. We also examine the genetic and epigenetic association of CRIP1a within a variety of cancer subtypes. This review provides evidence upon which to base future investigations on the function of CRIP1a in health and disease.

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