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Journal ArticleDOI

The multiple roles of histidine in protein interactions

01 Mar 2013-Chemistry Central Journal (BioMed Central)-Vol. 7, Iss: 1, pp 44-44
TL;DR: The coordinate interactions between histidine and metallic cations are the strongest one acting in broad range, followed by the cation-π, hydrogen-π), and π-π stacking interactions.
Abstract: Among the 20 natural amino acids histidine is the most active and versatile member that plays the multiple roles in protein interactions, often the key residue in enzyme catalytic reactions. A theoretical and comprehensive study on the structural features and interaction properties of histidine is certainly helpful. Four interaction types of histidine are quantitatively calculated, including: (1) Cation-π interactions, in which the histidine acts as the aromatic π-motif in neutral form (His), or plays the cation role in protonated form (His+); (2) π-π stacking interactions between histidine and other aromatic amino acids; (3) Hydrogen-π interactions between histidine and other aromatic amino acids; (4) Coordinate interactions between histidine and metallic cations. The energies of π-π stacking interactions and hydrogen-π interactions are calculated using CCSD/6-31+G(d,p). The energies of cation-π interactions and coordinate interactions are calculated using B3LYP/6-31+G(d,p) method and adjusted by empirical method for dispersion energy. The coordinate interactions between histidine and metallic cations are the strongest one acting in broad range, followed by the cation-π, hydrogen-π, and π-π stacking interactions. When the histidine is in neutral form, the cation-π interactions are attractive; when it is protonated (His+), the interactions turn to repulsive. The two protonation forms (and pKa values) of histidine are reversibly switched by the attractive and repulsive cation-π interactions. In proteins the π-π stacking interaction between neutral histidine and aromatic amino acids (Phe, Tyr, Trp) are in the range from -3.0 to -4.0 kcal/mol, significantly larger than the van der Waals energies.
Citations
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TL;DR: In this article, the performance of the hybrid nanomaterials applied as adsorbents to remove malachite green (MG) as a cationic dye from colored wastewater was investigated.

440 citations

Journal ArticleDOI
TL;DR: The findings of this study can facilitate rational drug design targeting the SARS-CoV-2 main protease, including carfilzomib, eravacycline, valrubicin, lopinavir, and elbasvir.
Abstract: The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes possible treatment strategies using drugs on the market. It is very efficient to apply computer-aided drug design techniques to quickly identify promising drug repurposing candidates, especially after the detailed 3D structures of key viral proteins are resolved. The virus causing COVID-19 is SARS-CoV-2. Taking advantage of a recently released crystal structure of SARS-CoV-2 main protease in complex with a covalently bonded inhibitor, N3 (Liu et al., 10.2210/pdb6LU7/pdb), I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an end point method called MM-PBSA-WSAS (molecular mechanics/Poisson-Boltzmann surface area/weighted solvent-accessible surface area; Wang, Chem. Rev. 2019, 119, 9478; Wang, Curr. Comput.-Aided Drug Des. 2006, 2, 287; Wang; ; Hou J. Chem. Inf. Model., 2012, 52, 1199). Several promising known drugs stand out as potential inhibitors of SARS-CoV-2 main protease, including carfilzomib, eravacycline, valrubicin, lopinavir, and elbasvir. Carfilzomib, an approved anticancer drug acting as a proteasome inhibitor, has the best MM-PBSA-WSAS binding free energy, -13.8 kcal/mol. The second-best repurposing drug candidate, eravacycline, is synthetic halogenated tetracycline class antibiotic. Streptomycin, another antibiotic and a charged molecule, also demonstrates some inhibitory effect, even though the predicted binding free energy of the charged form (-3.8 kcal/mol) is not nearly as low as that of the neutral form (-7.9 kcal/mol). One bioactive, PubChem 23727975, has a binding free energy of -12.9 kcal/mol. Detailed receptor-ligand interactions were analyzed and hot spots for the receptor-ligand binding were identified. I found that one hot spot residue, His41, is a conserved residue across many viruses including SARS-CoV, SARS-CoV-2, MERS-CoV, and hepatitis C virus (HCV). The findings of this study can facilitate rational drug design targeting the SARS-CoV-2 main protease.

376 citations


Cites background from "The multiple roles of histidine in ..."

  • ...43 After the sulfide bond is formed as a result of nucleophilic attack on catalytic Cys145 by the N3 ligand, His41 can stabilize the ligand−protein interaction by forming π−π stacking interactions between the His41 and the benzene motif of N3....

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Journal ArticleDOI
TL;DR: ZIF-67 was able to remove MG from the aquaculture wastewater, in which MG can be typically found, and could be conveniently regenerated by washing with ethanol and the regeneration efficiency could remain 95% up to 4 cycles of the regeneration.

331 citations

Journal ArticleDOI
TL;DR: This guide will help triage candidate methods for peptide alteration and will serve as a starting point for those seeking to solve long-standing challenges.
Abstract: Advances in bioconjugation and native protein modification are appearing at a blistering pace, making it increasingly time consuming for practitioners to identify the best chemical method for modifying a specific amino acid residue in a complex setting. The purpose of this perspective is to provide an informative, graphically rich manual highlighting significant advances in the field over the past decade. This guide will help triage candidate methods for peptide alteration and will serve as a starting point for those seeking to solve long-standing challenges.

320 citations

Journal ArticleDOI
TL;DR: The enriched nutrition knowledge base would enhance the utility of fish as a source of quality animal proteins and amino acids and aid in their inclusion in dietary counseling and patient guidance for specific nutritional needs.
Abstract: Proteins and amino acids are important biomolecules which regulate key metabolic pathways and serve as precursors for synthesis of biologically important substances; moreover, amino acids are building blocks of proteins. Fish is an important dietary source of quality animal proteins and amino acids and play important role in human nutrition. In the present investigation, crude protein content and amino acid compositions of important food fishes from different habitats have been studied. Crude protein content was determined by Kjeldahl method and amino acid composition was analyzed by high performance liquid chromatography and information on 27 food fishes was generated. The analysis showed that the cold water species are rich in lysine and aspartic acid, marine fishes in leucine, small indigenous fishes in histidine, and the carps and catfishes in glutamic acid and glycine. The enriched nutrition knowledge base would enhance the utility of fish as a source of quality animal proteins and amino acids and aid in their inclusion in dietary counseling and patient guidance for specific nutritional needs.

150 citations


Cites background from "The multiple roles of histidine in ..."

  • ...Histidine plays multiple roles in protein interaction [27] and is also a precursor of histamine....

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References
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Journal ArticleDOI
TL;DR: In this article, a method is presented which utilizes the calculation of the molecular electrostatic potential or the electric field at a discrete number of preselected points to evaluate the environmental effects of a solvent on the properties of a molecular system.

7,618 citations


"The multiple roles of histidine in ..." refers background or methods in this paper

  • ...The calculated values of PCM may be not very accurate, but the qualitative order is meaningful....

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  • ...The PCM is a continuum medium model [50-53]....

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  • ...In recent years great efforts are made to make up the shortcoming of DFT in dispersion interactions, including design of new functional [47], or empirical correction terms [41,42,48-50]....

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  • ...Based on our calculations by using PCM method, the energies of cation-π interactions decrease sharply with the increase of the dielectric constant ε of solvents....

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  • ...The interaction energies in solutions are calculated by using the polarizable continuum model (PCM) [50-53]....

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Journal ArticleDOI
TL;DR: The coupled cluster singles and doubles model (CCSD) as discussed by the authors is derived algebraically, presenting the full set of equations for a general reference function explicitly in spin-orbital form, and the computational implementation of the CCSD model, which involves cubic and quartic terms, is discussed and results are compared with full CI calculations for H2O and BeH2.
Abstract: The coupled‐cluster singles and doubles model (CCSD) is derived algebraically, presenting the full set of equations for a general reference function explicitly in spin–orbital form. The computational implementation of the CCSD model, which involves cubic and quartic terms, is discussed and results are reported and compared with full CI calculations for H2O and BeH2. We demonstrate that the CCSD exponential ansatz sums higher‐order correlation effects efficiently even for BeH2, near its transition state geometry where quasidegeneracy efforts are quite large, recovering 98% of the full CI correlation energy. For H2O, CCSD plus the fourth‐order triple excitation correction agrees with the full CI energy to 0.5 kcal/mol. Comparisons with low‐order models provide estimates of the effect of the higher‐order terms T1T2, T21T2, T31, and T41 on the correlation energy.

5,603 citations


"The multiple roles of histidine in ..." refers background or result in this paper

  • ...On the other hand, the more advanced coupled-cluster with single and double CCSD and triple excitations CCSD(T) methods [43-46] are able to evaluate the dispersion interaction well....

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  • ...Our and other authors’ comparison calculations revealed that π-π stacking interactions are dispersion-dominated phenomenon [43-46]....

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Book
01 Jun 1977
TL;DR: Localized Chemical bonding Delocalized Chemical Bonding Bonding Weaker than Covalent Stereochemistry Carbocations, Carbanions, Free Radicals, Carbenes and Nitrenes Mechanisms and Methods of Determining them Photochemistry Acids and Bases Effects of Structure on Reactivity Aliphatic Nucleophilic Substitution Aromatic Electrophilic Substitutes Aliphatically Electrophilic Substitution Free-Radical Substitution Addition to Carbon-Carbon Multiple Bonds Adding to Carbon Hetero Multiple Bonds Eliminations Rearrangements Ox
Abstract: Localized Chemical bonding Delocalized Chemical Bonding Bonding Weaker than Covalent Stereochemistry Carbocations, Carbanions, Free Radicals, Carbenes and Nitrenes Mechanisms and Methods of Determining Them Photochemistry Acids and Bases Effects of Structure on Reactivity Aliphatic Nucleophilic Substitution Aromatic Electrophilic Substitution Aliphatic Electrophilic Substitution Free-Radical Substitution Addition to Carbon-Carbon Multiple Bonds Addition to Carbon- Hetero Multiple Bonds Eliminations Rearrangements Oxidations and Reductions The Literature of Organic Chemistry Classifications of Reactions by Type of Compound Synthesized.

4,885 citations

Journal ArticleDOI
TL;DR: The DFT‐D‐BLYP model seems to be even superior to standard MP2 treatments that systematically overbind, and the approach is suggested as a practical tool to describe the properties of many important van der Waals systems in chemistry.
Abstract: An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R−6. The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The “double counting” of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene · H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1463–1473, 2004

4,332 citations


"The multiple roles of histidine in ..." refers background in this paper

  • ...In DNA the π-π stacking interactions have larger contributions than in proteins [41,47-49]....

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  • ...In recent years great efforts are made to make up the shortcoming of DFT in dispersion interactions, including design of new functional [47], or empirical correction terms [41,42,48-50]....

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Journal ArticleDOI
TL;DR: In this paper, a geometrical analysis of π-π stacking in metal complexes with aromatic nitrogen-containing ligands was performed based on a Cambridge Structural Database search and on X-ray data of examples.
Abstract: A geometrical analysis has been performed on π–π stacking in metal complexes with aromatic nitrogen-containing ligands based on a Cambridge Structural Database search and on X-ray data of examples in the recent literature. It is evident that a face-to-face π–π alignment where most of the ring-plane area overlaps is a rare phenomenon. The usual π interaction is an offset or slipped stacking, i.e. the rings are parallel displaced. The ring normal and the vector between the ring centroids form an angle of about 20° up to centroid–centroid distances of 3.8 A. Such a parallel-displaced structure also has a contribution from π–σ attraction, the more so with increasing offset. Only a limited number of structures with a near to perfect facial alignment exists. The term π–π stacking is occasionally used even when there is no substantial overlap of the π-ring planes. There is a number of metal–ligand complexes where only the edges of the rings interact in what would be better described a C–H⋯π attraction.

3,881 citations


"The multiple roles of histidine in ..." refers background in this paper

  • ...However, the cation-π interaction energies of His are smaller than that of other three aromatic amino acids (Phe, Tyr, and Trp) because of the smaller π-system size [57,58]....

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  • ...The imidazole structure of histidine side chain is a conjugative π-plane, which can make π-π stacking interactions with the aromatic side chains of other amino acids (Phe, Tyr, and Trp) [20,21]....

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  • ...The π-π stacking interactions between neutral His and aromatic amino acids (Phe, Tyr, and Trp) are in the range −3.0 to −4.0 kcal/mol, significantly larger than the van der Waals interactions....

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  • ...The π-π stacking interactions in proteins are a controversial research topic [17-21]....

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  • ...(Organic cation) Energy a Length d Energy a Length d Phe −7.809 3.269 −3.613 4.809 Tyr −7.887 3.256 −3.655 4.799 Trp −13.642 3.166 −12.057 3.276 a Energies are in kcal/mol, calculated using B3LYP/6-31+G(d,p) method. b Angstrom (Å). c Distance from N of CH3NH3 + (or CHNH2NH2 +) to the center of imidazole ring. d Distance from N of imidazole to the aromatic center of amino acids (Phe, Tyr, and Trp). chain, obtained from CCSD calculations, are combined with the parameters of DFT optimizations....

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