scholarly journals Hydrophobicity Revisited: a Molecular Story

2020 ◽  
Author(s):  
David Cavanaugh ◽  
Krishnan Chittur
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Amino Acid ◽  
Linear Regression ◽  
Group Structure ◽  
Chemical Properties ◽  
Molecular Geometry ◽  
Superior Performance ◽  
Acid Property ◽  
Physico Chemical

In a previous paper we have introduced a new hydrophobicity proclivity scale and justified its superior performance characteristics, particularly in the context of a scale for protein alignments, but also for its strong correlation with many other amino-acid physico-chemical properties. Within that paper, we calculated a corrected free energy of residue burial of each amino-acid in folded proteins from a linear regression of amino-acid free energy of transfer from water to n-Octanol (F&P octanol scale dGow, Y axis) and our Hydrophobicity Proclivity Scale<br>(HPS, X axis). In this present paper we pursue the latter general findings in more detail by considering the relationship of hydrophobicity and other physico-amino-<br>acid scales with the molecular geometry of amino-acids and secondary group structure/surface chemistry, with a concommitant discussion of the dimensions/geometry<br>of the caveties that amino-acids make in water. We identify a series of molecular physico-chemical properties that uniquely define the natural selection and geometry of the 20 natural amino-acids. We use the corrected free energy of amino-acid burials in proteins (Y axis) and a multiple linear regression to identify the AA molecular physico-chemical properties (X1, X2, ...) that explain the energetics of amino-<br>acid water contacts in an unfolded protein state to that of the folded protein state by modeling these two states as a solvent-solvent transfer, thus, providing a thermodynamical model for the initial stages of protein folding. Between our previous paper and the current paper we can greatly simplify and reduce the very large number of amino-acid scales in the literature to a small number of amino-acid property scales. Finally, we explore the numerical relationship between the structure of the genetic code and molecular physico-chemical properties of AA’s that in turn can be related directly to hydrophobicity. We validate and explain our novel models we describe herein with extensive data from the literature.<br>

scholarly journals Hydrophobicity Revisited: a Molecular Story

2020 ◽  
Author(s):  
David Cavanaugh ◽  
Krishnan Chittur
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Amino Acid ◽  
Linear Regression ◽  
Group Structure ◽  
Chemical Properties ◽  
Molecular Geometry ◽  
Superior Performance ◽  
Acid Property ◽  
Physico Chemical

In a previous paper we have introduced a new hydrophobicity proclivity scale and justified its superior performance characteristics, particularly in the context of a scale for protein alignments, but also for its strong correlation with many other amino-acid physico-chemical properties. Within that paper, we calculated a corrected free energy of residue burial of each amino-acid in folded proteins from a linear regression of amino-acid free energy of transfer from water to n-Octanol (F&P octanol scale dGow, Y axis) and our Hydrophobicity Proclivity Scale<br>(HPS, X axis). In this present paper we pursue the latter general findings in more detail by considering the relationship of hydrophobicity and other physico-amino-<br>acid scales with the molecular geometry of amino-acids and secondary group structure/surface chemistry, with a concommitant discussion of the dimensions/geometry<br>of the caveties that amino-acids make in water. We identify a series of molecular physico-chemical properties that uniquely define the natural selection and geometry of the 20 natural amino-acids. We use the corrected free energy of amino-acid burials in proteins (Y axis) and a multiple linear regression to identify the AA molecular physico-chemical properties (X1, X2, ...) that explain the energetics of amino-<br>acid water contacts in an unfolded protein state to that of the folded protein state by modeling these two states as a solvent-solvent transfer, thus, providing a thermodynamical model for the initial stages of protein folding. Between our previous paper and the current paper we can greatly simplify and reduce the very large number of amino-acid scales in the literature to a small number of amino-acid property scales. Finally, we explore the numerical relationship between the structure of the genetic code and molecular physico-chemical properties of AA’s that in turn can be related directly to hydrophobicity. We validate and explain our novel models we describe herein with extensive data from the literature.<br>

scholarly journals Porin from Marine Bacterium Marinomonas primoryensis KMM 3633T: Isolation, Physico-Chemical Properties, and Functional Activity

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3131
Author(s):  
Olga D. Novikova ◽  
Valentina A. Khomenko ◽  
Natalia Yu. Kim ◽  
Galina N. Likhatskaya ◽  
Lyudmila A. Romanenko ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Lipid Membranes ◽  
Marine Bacterium ◽  
Chemical Properties ◽  
Cell Permeability ◽  
Oligomeric Structure ◽  
Black Lipid Membranes ◽  
Physico Chemical ◽  
Coastal Sea

Marinomonas primoryensis KMM 3633T, extreme living marine bacterium was isolated from a sample of coastal sea ice in the Amursky Bay near Vladivostok, Russia. The goal of our investigation is to study outer membrane channels determining cell permeability. Porin from M. primoryensis KMM 3633T (MpOmp) has been isolated and characterized. Amino acid analysis and whole genome sequencing were the sources of amino acid data of porin, identified as Porin_4 according to the conservative domain searching. The amino acid composition of MpOmp distinguished by high content of acidic amino acids and low content of sulfur-containing amino acids, but there are no tryptophan residues in its molecule. The native MpOmp existed as a trimer. The reconstitution of MpOmp into black lipid membranes demonstrated its ability to form ion channels whose conductivity depends on the electrolyte concentration. The spatial structure of MpOmp had features typical for the classical gram-negative porins. However, the oligomeric structure of isolated MpOmp was distinguished by very low stability: heat-modified monomer was already observed at 30 °C. The data obtained suggest the stabilizing role of lipids in the natural membrane of marine bacteria in the formation of the oligomeric structure of porin.

scholarly journals Amino Acid, Fatty Acid and Physico-Chemical Analyses of Jatropha curcas (Physic Nut) Seed Flour and Oil

1970 ◽  
Vol 45 (4) ◽  
pp. 345-350 ◽  
Author(s):  
O Olaofe ◽  
FJ Faleye ◽  
JA Abey
Keyword(s):  
Amino Acids ◽  
Fatty Acid ◽  
Amino Acid ◽  
Saturated Fatty Acid ◽  
Unsaturated Fatty Acid ◽  
Jatropha Curcas ◽  
Chemical Properties ◽  
Physic Nut ◽  
Seed Flour ◽  
Physico Chemical

The amino acid of seed flour and fatty acid and physico-chemical analysis of oil both from Jatropha curcas (physic nut) seed were analytically determined. Amino acid results showed that the protein contained nutritionally useful quantities of most of the essential amino acids including sulphur-containing amino acids. The crude protein content was 34.2%. The total essential amino acid (TEAA) with histidine was 32.7g /100g while the TEAA without histidine was 30.6g /100g protein. Glutamic acid (16.8 g/100g protein) was found to be the most abundant amino acid followed by aspartic acid (9.2 g/100g protein) in the seed flour. The seed oil of Jatropha curcas has a high crude fat content of 46.1% and a high proportion of total unsaturated fatty acid (40.8%) with liloleic (18:2) as the most abundant unsaturated fatty acid while the total saturated fatty acid was 8.61% Palmitic acid (16:0), 8.6 % was found to be the most abundant saturated fatty acid. The values for the physico-chemical properties of the extracted oil were: Acid value, (4.62 mgKOH/g), iodine value, (96.0 mgI2/g), peroxide value, (6.22 mgO2/g), saponification value, (219 mg KOH/g), specific gravity, (0.89) and refractive index, (1.46), These results suggest that Jatropha curcas is useful in some food formulations. Key words:. DOI: 10.3329/bjsir.v45i4.7379 Bangladesh J. Sci. Ind. Res. 45(4), 345-350, 2010

Amino acid composition and physico-chemical properties of bluefin tuna (Thunnus thynnus) myoglobin

1978 ◽  
Vol 60 (2) ◽  
pp. 195-199 ◽  
Author(s):  
Ciro Balestrieri ◽  
Giovanni Colonna ◽  
Alfonso Giovane ◽  
Gaetano Irace ◽  
Luigi Servillo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Chemical Properties ◽  
Bluefin Tuna ◽  
Thunnus Thynnus ◽  
Physico Chemical

Self-healing hydrogels triggered by amino acids

2016 ◽  
Vol 3 (12) ◽  
pp. 1699-1704 ◽  
Author(s):  
Nicola Zanna ◽  
Andrea Merlettini ◽  
Claudia Tomasini
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aspartic Acid ◽  
Chemical Properties ◽  
Aromatic Amino Acids ◽  
Self Healing ◽  
Acidic Amino Acid ◽  
Basic Amino Acids

Nine amino acids with different chemical properties have been chosen to promote the formation of hydrogels based on the bolamphiphilic gelator A: three basic amino acids (arginine, histidine and lysine), one acidic amino acid (aspartic acid), two neutral aliphatic amino acids (alanine and serine) and three neutral aromatic amino acids (phenylalanine, tyrosine and tryptophan).

scholarly journals Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins

Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1032
Author(s):  
Sonia Khemaissa ◽  
Sandrine Sagan ◽  
Astrid Walrant
Keyword(s):  
Amino Acid ◽  
Membrane Proteins ◽  
Hydrogen Bonds ◽  
Membrane Protein ◽  
Lipid Bilayers ◽  
Noncovalent Interactions ◽  
Chemical Properties ◽  
Protein Stabilization ◽  
Physico Chemical

Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.

Capillary Gas Chromatographic Analysis of Amino Acids by Enantiomer Labeling

1987 ◽  
Vol 70 (2) ◽  
pp. 234-240
Author(s):  
Ernst Bayer ◽  
Hartmut Frank ◽  
Jürgen Gerhardt ◽  
Graeme Nicholson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sea Water ◽  
Biological Fluids ◽  
Chemical Properties ◽  
Internal Standard ◽  
Optical Isomers ◽  
Internal Standards ◽  
Sample Enrichment ◽  
Physical And Chemical

Abstract The optical isomers of amino acids can be easily separated by gas chromatography using capillary columns coated with the chiral polysiloxane peptide, Chirasil-Val. Quantitative trace amino acid analysis in complex mixtures such as biological fluids, sea water, or protein hydrolysates can be achieved by enantiomer labeling: The D-amino acid enantiomers, which do not occur naturally, are added to the sample prior to analysis as internal standards. Because the D-enantiomers show the same physical and chemical properties as the natural L-enantiomers, they are ideal standard references. In routine analysis, the derivatization is achieved with a new automated derivatization robot. The D-standard serves as overall internal standard for the whole analytical procedure from sample enrichment to derivatization, chromatography, and response of the detector.

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