Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data

The understanding of electron transport in proteins based on a novel technique involving muon spin rotation (μSR)measurements is a topic of great current interest. The technique, which involves study of spin relaxation of a positive muon (μ+) trapped in amino acids in protein chains due to the fluctuating magnetic field that the moving electron produces, is based on the premise that the electron is generated by ionization of a muonium (Mu) which was trapped at the same site as the μ+ left behind. In attempting to test this premise from first-principles for the Cytochrome c (Cyt c) system in which recent μSR measurements have been made, we have carried out Hartree- Fock investigations of the electronic structures of the bare amino acids and amino acids with + and Mu trapped at the oxygen of the C=O group common to all amino acids. With the aim that the comparison of theoretically predicted experimental nuclear quadrupole interaction (NQI) parameters will provide a useful test of the electron distribution in the amino acids of Cyt c, we present results for the nuclear quadrupole coupling constants (e2qQ) and asymmetry parameters (η) for the bare amino acids and the amino acids with trapped μ+ and Mu. The trends in 2 and for 14N and 17O between the various amino acids, as well as the changes in these parameters in the presence of μ+ and Mu are being analyzed. It would be helpful to have experimental data for e2qQ and to η compare with our predictions for the amino acids as they occur in vitro in polycrystalline Cyt c in which the SR measurements have been carried out. It is also hoped that the μSR technique will be able to provide experimental data on e2qQ and for the 14N and 17O nuclei to compare with our predictions

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Effect of Hydroxylamine Sulfate on Volumetric Behavior of Glycine,L-Alanine, andL-Arginine in Aqueous Solution

Journal of Chemistry ◽

10.1155/2013/481341 ◽

2013 ◽

Vol 2013 ◽

pp. 1-5 ◽

Cited By ~ 3

Author(s):

Jie Chen ◽

Sheng Fang ◽

Yu-Gang Shi ◽

Yue-Cheng Meng ◽

Da-Hai Ren

Keyword(s):

Experimental Data ◽

Amino Acids ◽

Atmospheric Pressure ◽

Partial Molar Volumes ◽

Hydration Numbers ◽

Molar Volumes ◽

Mixing Effects ◽

Sulfate Solutions ◽

Volumetric Behavior ◽

Hydroxylamine Sulfate

The apparent molar volumes of glycine,L-alanine, andL-arginine in aqueous hydroxylamine sulfate solutions have been determined atT=298.15 K and atmospheric pressure. The standard partial molar volumes,V20, corresponding partial molar volumes of transfer,ΔtrV20, and hydration numbers,NH, have been calculated for theseα-amino acids from the experimental data. TheΔtrV20values are positive for glycine,L-alanine, andL-arginine and are all increased with the increase in the concentration of hydroxylamine ions. These parameters obtained from the volumetric data are interpreted in terms of various mixing effects between amino acids and hydroxylamine sulfate in aqueous solutions.

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Investigations on the Effects of Salts and Carbohydrates on L-Lysine in Aqueous System at T=293.15K

Oriental Journal Of Chemistry ◽

10.13005/ojc/370327 ◽

2021 ◽

Vol 37 (3) ◽

pp. 704-709

Author(s):

Rajesh Kumar Sharma ◽

Priyanka Sharma

Keyword(s):

Experimental Data ◽

Amino Acids ◽

Surface Tension ◽

Sodium Chloride ◽

Physicochemical Parameters ◽

Aqueous System ◽

Specific Conductance ◽

Stabilization Mechanism ◽

Solvent Interactions ◽

Physicochemical Studies

Physicochemical studies of amino acids in an aqueous medium can provide significant knowledge about the stabilization mechanism of proteins.In this study, the viscosity (ƞ), surface tension (γ), density (ρ) and the specific conductance (κ) measurements have been carried out for amino acid L-lysine (0.02 to 1.6M) in aqueous solutions at 293.15K. The experimental data shows that there is an increase in the viscosity, surface tension, conductance, and density of the L-lysine with and without glucose, sucrose, sodium chloride, and potassium chloride with concentration.The solute-solute and solute-solvent interactions have been discussed on the basis of all physicochemical parameters.

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Die primäre Proteinstruktur von Stämmen des Tabakmosaikvirus

Zeitschrift für Naturforschung B ◽

10.1515/znb-1969-0716 ◽

1969 ◽

Vol 24 (7) ◽

pp. 877-885 ◽

Cited By ~ 16

Author(s):

H. G. Wittmann ◽

I. Hindennach ◽

B. Wittmann-Liebold

Keyword(s):

Experimental Data ◽

Amino Acids ◽

Amino Acid ◽

Coat Protein ◽

Amino Acid Sequence ◽

Spatial Structure ◽

Amino Acid Sequences ◽

The Other ◽

Tryptic Peptides ◽

Tmv Strains

Experimental data for determining a) the amino acid sequences of eight tryptic peptides containing 95 amino acids and b) the order of the tryptic peptides are given. Combining the data of this and of a previous paper the complete amino acid sequence of the coat protein of the TMV strain Holmes rib grass (HRG) is established (Fig. 5). It is compared with three other TMV strains the sequences of which have been determined before (Fig. 6).Differences and similarities between the sequences of the four TMV strains are discussed. HRG has a deletion of two amino acids and it is the most distantly related of the four TMV strains. When the sequence of HRG is compared to that of any of the other strains it turns out that in each case more than 50% of the 156 positions contain different amino acids (Fig. 7).The number of positions with the same amino acid in all strains and mutants so far studied is 30 per cent. These positions are not randomly distributed but clustered mainly in two regions. This finding probably reflects the restriction of amino acid exchanges by the spatial structure of the viral rod.

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Estimation of biomass composition from genomic and transcriptomic information

Journal of Integrative Bioinformatics ◽

10.1515/jib-2016-285 ◽

2016 ◽

Vol 13 (2) ◽

pp. 1-14 ◽

Cited By ~ 3

Author(s):

Sophia Santos ◽

Isabel Rocha

Keyword(s):

Experimental Data ◽

Amino Acids ◽

Metabolic Model ◽

Good Alternative ◽

Biomass Composition ◽

Biomass Equation ◽

Transcriptomic Data ◽

Balance Analysis ◽

User Friendly ◽

Genome Information

SummaryGiven the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genomescale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments. In this work a java tool is proposed that estimates microbial biomass composition in amino acids and nucleotides, from genome and transcriptomic information, using as input files sequences in FASTA format and files with transcriptomic data in the csv format. This application allows to obtain the results rapidly and is also a user-friendly tool for users with any or little background in informatics (http://darwin.di.uminho.pt/biomass/). The results obtained using this tool are fairly close to experimental data, showing that the estimation of amino acid and nucleotide compositions from genome information and from transcriptomic data is a good alternative when no experimental data is available.

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Determinants of spironolactone binding specificity in the mineralocorticoid receptor

Journal of Molecular Endocrinology ◽

10.1677/jme.0.0310573 ◽

2003 ◽

Vol 31 (3) ◽

pp. 573-582 ◽

Cited By ~ 26

Author(s):

FM Rogerson ◽

YZ Yao ◽

BJ Smith ◽

N Dimopoulos ◽

PJ Fuller

Keyword(s):

Crystal Structure ◽

Experimental Data ◽

Amino Acids ◽

Ligand Binding ◽

Mineralocorticoid Receptor ◽

Binding Specificity ◽

Binding Pocket ◽

Clinical Use ◽

Ligand Binding Pocket ◽

Binding Domains

Spironolactone is a mineralocorticoid receptor (MR) antagonist in clinical use. The compound has a very low affinity for the glucocorticoid receptor (GR). Determinants of binding specificity of spironolactone to the MR were investigated using chimeras created between the ligand-binding domains (LBDs) of the MR and the GR. These chimeras had previously been used to investigate aldosterone binding specificity to the MR. Spironolactone was able to compete strongly for [(3)H]-aldosterone and [(3)H]-dexamethasone binding to a chimera containing amino acids 804-874 of the MR, and weakly for [(3)H]-dexamethasone binding to a chimera containing amino acids 672-803 of the MR. Amino acids 804-874 were also critical for aldosterone binding specificity. Models of the MR LBD bound to aldosterone and spironolactone were created based on the crystal structure of the progesterone receptor LBD. The ligand-binding pocket of the MR LBD model consisted of 23 amino acids and was predominantly hydrophobic in nature. Analysis of this model in light of the experimental data suggested that spironolactone binding specificity is not governed by amino acids in the ligand-binding pocket.

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Evolution of frustrated and stabilising contacts in reconstructed ancient proteins

European Biophysics Journal ◽

10.1007/s00249-021-01500-0 ◽

2021 ◽

Author(s):

Martina Crippa ◽

Damiano Andreghetti ◽

Riccardo Capelli ◽

Guido Tiana

Keyword(s):

Amino Acids ◽

Protein Stability ◽

Interaction Network ◽

Reconstruction Algorithm ◽

Major Determinant ◽

Evolutionary Time ◽

Energetic Properties ◽

Ancient Proteins ◽

Evolutionary Fitness

AbstractEnergetic properties of a protein are a major determinant of its evolutionary fitness. Using a reconstruction algorithm, dating the reconstructed proteins and calculating the interaction network between their amino acids through a coevolutionary approach, we studied how the interactions that stabilise 890 proteins, belonging to five families, evolved for billions of years. In particular, we focused our attention on the network of most strongly attractive contacts and on that of poorly optimised, frustrated contacts. Our results support the idea that the cluster of most attractive interactions extends its size along evolutionary time, but from the data, we cannot conclude that protein stability or that the degree of frustration tends always to decrease.

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