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Nekrasova NA, Kurbatova SV. Quantitative structure–chromatographic retention correlations of quinoline derivatives. J Chromatogr A 2017; 1492:55-60. [DOI: 10.1016/j.chroma.2017.02.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/07/2017] [Accepted: 02/26/2017] [Indexed: 12/19/2022]
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2
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Iwashita K, Shiraki K, Ishii R, Tanaka T, Hirano A. Liquid Chromatographic Analysis of the Interaction between Amino Acids and Aromatic Surfaces Using Single-Wall Carbon Nanotubes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015. [PMID: 26208035 DOI: 10.1021/acs.langmuir.5b02500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins have nonspecific adsorption capacities for solid surfaces. Although the nonspecific adsorption capacities are generally understood to be related to the hydrophobicity or charge density of the surfaces, little is known at the amino acid level about the interaction between proteins and polyaromatic surfaces such as carbon nanotubes, which have recently been used for biotechnology applications. In this study, we investigated the interaction between proteinogenic amino acids and carbon nanotubes using high-performance liquid chromatography on silica matrices coated by single-wall carbon nanotubes (SWCNTs). Among the amino acids used in this study, tryptophan, tyrosine, and phenylalanine showed exceptional affinity for the matrices. The characteristic affinities of these amino acids were ascribed to their unique interactions with the large polyaromatic surfaces of the SWCNTs. These results are useful for understanding and controlling protein adsorption onto aromatic surfaces.
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Affiliation(s)
- Kazuki Iwashita
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kentaro Shiraki
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Rieko Ishii
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Takeshi Tanaka
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Atsushi Hirano
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
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Li HW, Wang Y, Zhang T, Wu Y, Wu L. Selective Binding of Amino Acids on Europium-Substituted Polyoxometalates and the Interaction-Induced Luminescent Enhancement Effect. Chempluschem 2014. [DOI: 10.1002/cplu.201402091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Markopoulou CK, Kouskoura MG, Koundourellis JE. Modelling by partial least squares the relationship between the HPLC mobile phases and analytes on phenyl column. J Sep Sci 2011; 34:1489-502. [DOI: 10.1002/jssc.201100091] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 11/09/2022]
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5
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QSAR in Chromatography: Quantitative Structure–Retention Relationships (QSRRs). CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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6
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Liu X, Liang J, Fan J, Shang Z. Prediction of Ion Drift Times for a Proteome-Wide Peptide Set Using Partial Least Squares Regression, Least-Squares Support Vector Machine and Gaussian Process. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200910075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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7
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Affiliation(s)
- Roman Kaliszan
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera 107, 80416 Gdańsk, Poland.
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Camargo AB, Marchevsky E, Luco JM. QSAR study for the soybean 15-lipoxygenase inhibitory activity of organosulfur compounds derived from the essential oil of garlic. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:3096-103. [PMID: 17367159 DOI: 10.1021/jf063020e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In this study, multiple linear regression (MLR) and partial least-squares (PLS) techniques were used for modeling the soybean 15-lipoxygenase inhibitory activity of a varied group of mono-, di-, and trisulfides derived from the essential oil of garlic. The structures of the compounds under study were characterized by means of calculated physicochemical parameters and several nonempirical descriptors, such as topological, geometrical, and quantum chemical indices. The results obtained indicate that the inhibitory activity is strongly dependent on the ability of the compounds to participate in dispersive interactions with the enzyme, as expressed by the solvent-accessible surface area (SASA) and the average distance/distance degree descriptor (ADDD) index. On the other hand, the high contribution of the lowest unoccupied molecular orbit term (LUMO) in the PLS models derived for the di- and trisulfides suggests that the solute's electron-acceptor capacity plays a fundamental role in the inhibitory activity exhibited for these compounds. Finally, the geometric features as expressed by the shape parameters included in the models indicate a low but not negligible positive contribution of molecular linearity in the enzyme-inhibitor binding. In summary, the developed quantitative structure-activity relationship approach successfully accounts for the potencies of organosulfur compounds acting on soybean 15-lipoxygenase and thereby offers both a guide for the synthesis of new compounds and a hypothesis for the molecular basis of their activity.
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Affiliation(s)
- Alejandra B Camargo
- Laboratorio de AnAlisis de Residuos Tóxicos, Facultad de Ciencia Agrarias, Universidad Nacional de Cuyo, Alte. Brown 500, Chacras de Coria 5505 Mendoza, Argentina
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9
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Abstract
The newest results in the application of various chromatographic methods (gas-liquid chromatography, liquid chromatographic techniques, electrically driven systems) for the separation and quantitative determination of amino acids and short peptides in pure state and in complicated matrices are compiled. The results are concisely described and critically evaluated. The future trends of the chromatographic analysis of amino acids and short peptides are briefly discussed.
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Affiliation(s)
- T Cserháti
- Research Institute of Materials and Environmental Chemistry, Chemical Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
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Tripet B, Cepeniene D, Kovacs JM, Mant CT, Krokhin OV, Hodges RS. Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location. J Chromatogr A 2006; 1141:212-25. [PMID: 17187811 PMCID: PMC2722105 DOI: 10.1016/j.chroma.2006.12.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 12/01/2006] [Accepted: 12/05/2006] [Indexed: 11/27/2022]
Abstract
The value of reversed-phase high-performance liquid chromatography (RP-HPLC) and the field of proteomics would be greatly enhanced by accurate prediction of retention times of peptides of known composition. The present study investigates the hydrophilicity/hydrophobicity of amino acid side-chains at the N- and C-termini of peptides while varying the functional end-groups at the termini. We substituted all 20 naturally occurring amino acids at the N- and C-termini of a model peptide sequence, where the functional end-groups were N(alpha)-acetyl-X- and N(alpha)-amino-X- at the N-terminus and -X-C(alpha)-carboxyl and -X-C(alpha)-amide at the C-terminus. Amino acid coefficients were subsequently derived from the RP-HPLC retention behaviour of these peptides and compared to each other as well as to coefficients determined in the centre of the peptide chain (internal coefficients). Coefficients generated from residues substituted at the C-terminus differed most (between the -X-C(alpha)-carboxyl and -X-C(alpha)-amide peptide series) for hydrophobic side-chains. A similar result was seen for the N(alpha)-acetyl-X- and N(alpha)-amino-X- peptide series, where the largest differences in coefficient values were observed for hydrophobic side-chains. Coefficients derived from substitutions at the C-terminus for hydrophobic amino acids were dramatically different compared to internal coefficients for hydrophobic side-chains, ranging from 17.1 min for Trp to 4.8 min for Cys. In contrast, coefficients derived from substitutions at the N-terminus showed relatively small differences from the internal coefficients. Subsequent prediction of peptide retention time, within an error of just 0.4 min, was achieved by a predictive algorithm using a combination of internal coefficients and coefficients for the C-terminal residues. For prediction of peptide retention time, the sum of the coefficients must include internal and terminal coefficients.
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Affiliation(s)
- Brian Tripet
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denverand Health Sciences Center, Aurora, CO, 80045, USA
| | - Dziuleta Cepeniene
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denverand Health Sciences Center, Aurora, CO, 80045, USA
| | - James M. Kovacs
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denverand Health Sciences Center, Aurora, CO, 80045, USA
| | - Colin T. Mant
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denverand Health Sciences Center, Aurora, CO, 80045, USA
| | - Oleg V. Krokhin
- Manitoba Centre for Proteomic and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robert S. Hodges
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denverand Health Sciences Center, Aurora, CO, 80045, USA
- Corresponding author. Tel.: +1 303 724 3253; fax: +1 303 724 3249. E-mail address: (R.S. Hodges)
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Kovacs JM, Mant CT, Kwok SC, Osguthorpe DJ, Hodges RS. Quantitation of the nearest-neighbour effects of amino acid side-chains that restrict conformational freedom of the polypeptide chain using reversed-phase liquid chromatography of synthetic model peptides with L- and D-amino acid substitutions. J Chromatogr A 2006; 1123:212-24. [PMID: 16712857 PMCID: PMC1976429 DOI: 10.1016/j.chroma.2006.04.092] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 04/18/2006] [Accepted: 04/28/2006] [Indexed: 10/24/2022]
Abstract
Side-chain backbone interactions (or "effects") between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects (i to i+1) in peptides through reversed-phase liquid chromatography (RP-HPLC) of model synthetic peptides, where L- and D-amino acids were substituted at the N-terminal end of the peptide sequence, adjacent to a L-Leu residue. These nearest-neighbour effects (expressed as the difference in retention times of L- and D-peptide diastereomers at pHs 2 and 7) were frequently dramatic, depending on the type of side-chain adjacent to the L-Leu residue, albeit such effects were independent of mobile phase conditions. No nearest-neighbour effects were observed when residue i is adjacent to a Gly residue. Calculation of minimum energy conformations of selected peptides supported the view that, whether a L- or D-amino acid is substituted adjacent to L-Leu, its orientation relative to this bulky Leu side-chain represents the most energetically favourable configuration. We believe that such energetically favourable, and different, configurations of L- and D-peptide diastereomers affect their respective interactions with a hydrophobic stationary phase, which are thus quantified by different RP-HPLC retention times. Side-chain hydrophilicity/hydrophobicity coefficients were generated in the presence of these nearest-neighbour effects and, despite the relative difference in such coefficients generated from peptides substituted with L- or D-amino acids, the relative difference in hydrophilicity/hydrophobicity between different amino acids in the L- or D-series is maintained. Overall, our results demonstrate that such nearest-neighbour effects can clearly restrict conformational space of an amino acid side-chain in a polypeptide chain.
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Affiliation(s)
- James M Kovacs
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA
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12
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Kovacs JM, Mant CT, Hodges RS. Determination of intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides in the absence of nearest-neighbor or conformational effects. Biopolymers 2006; 84:283-97. [PMID: 16315143 PMCID: PMC2744689 DOI: 10.1002/bip.20417] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Understanding the hydrophilicity/hydrophobicity of amino acid side chains in peptides/proteins is one the most important aspects of biology. Though many hydrophilicity/hydrophobicity scales have been generated, an "intrinsic" scale has yet to be achieved. "Intrinsic" implies the maximum possible hydrophilicity/hydrophobicity of side chains in the absence of nearest-neighbor or conformational effects that would decrease the full expression of the side-chain hydrophilicity/hydrophobicity when the side chain is in a polypeptide chain. Such a scale is the fundamental starting point for determining the parameters that affect side-chain hydrophobicity and for quantifying such effects in peptides and proteins. A 10-residue peptide sequence, Ac-X-G-A-K-G-A-G-V-G-L-amide, was designed to enable the determination of the intrinsic values, where position X was substituted by all 20 naturally occurring amino acids and norvaline, norleucine, and ornithine. The coefficients were determined by reversed-phase high-performance liquid chromatography using six different mobile phase conditions involving different pH values (2, 5, and 7), ion-pairing reagents, and the presence and absence of different salts. The results show that the intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides (proteins) is independent of pH, buffer conditions, or whether C(8) or C(18) reversed-phase columns were used for 17 side chains (Gly, Ala, Cys, Pro, Val, nVal, Leu, nLeu, Ile, Met, Tyr, Phe, Trp, Ser, Thr, Asn, and Gln) and dependent on pH and buffer conditions, including the type of salt or ion-pairing reagent for potentially charged side chains (Orn, Lys, His, Arg, Asp, and Glu).
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Affiliation(s)
- James M Kovacs
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, 80045, USA
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Luco JM, Salinas AP, Torriero AAJ, Vázquez RN, Raba J, Marchevsky E. Immobilized artificial membrane chromatography: quantitative structure-retention relationships of structurally diverse drugs. ACTA ACUST UNITED AC 2004; 43:2129-36. [PMID: 14632465 DOI: 10.1021/ci034123p] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chromatographic capacity factors (log k') for 32 structurally diverse drugs were determined by high performance liquid chromatography (HPLC) on a stationary phase composed of phospholipids, the so-called immobilized artificial membrane (IAM). In addition, quantitative structure-retention relationships (QSRR) were developed in order to explain the dependence of retention on the chemical structure of the neutral, acidic, and basic drugs considered in this study. The obtained retention data were modeled by means of multiple regression analysis (MLR) and partial least squares (PLS) techniques. The structures of the compounds under study were characterized by means of calculated physicochemical properties and several nonempirical descriptors. For the carboxylic compounds included in the analysis, the obtained results suggest that the IAM-retention is governed by hydrophobicity factors followed by electronic effects due to polarizability in second place. Further, from the analysis of the results obtained of two developed quantitative structure-permeability studies for 20 miscellaneous carboxylic compounds, it may be concluded that the balance between polarizability and hydrophobic effects is not the same toward IAM phases and biological membranes. These results suggest that the IAM phases could not be a suitable model in assessing the acid-membrane interactions. However, it is not possible to generalize this observation, and further work in this area needs to be done to obtain a full understanding of the partitioning of carboxylic compounds in biological membranes. For the non-carboxylic compounds included in the analysis, this work shows that the hydrophobic factors are of prime importance for the IAM-retention of these compounds, while the specific polar interactions, such as electron pair donor-acceptor interactions and electrostatic interactions, are also involved, but they are not dominant.
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Affiliation(s)
- Juan M Luco
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco y Pedernera 5700 San Luis, Argentina.
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14
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Biswas KM, DeVido DR, Dorsey JG. Evaluation of methods for measuring amino acid hydrophobicities and interactions. J Chromatogr A 2003; 1000:637-55. [PMID: 12877193 DOI: 10.1016/s0021-9673(03)00182-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The concept of hydrophobicity has been addressed by researchers in all aspects of science, particularly in the fields of biology and chemistry. Over the past several decades, the study of the hydrophobicity of biomolecules, particularly amino acids has resulted in the development of a variety of hydrophobicity scales. In this review, we discuss the various methods of measuring amino acid hydrophobicity and provide explanations for the wide range of rankings that exist among these published scales. A discussion of the literature on amino acid interactions is also presented. Only a surprisingly small number of papers exist in this rather important area of research; measuring pairwise amino acid interactions will aid in understanding structural aspects of proteins.
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Affiliation(s)
- Kallol M Biswas
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
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15
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Barberis S, Quiroga E, Arribére MC, Priolo N. Peptide synthesis in aqueous–organic biphasic systems catalyzed by a protease isolated from Morrenia brachystephana (Asclepiadaceae). ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1381-1177(01)00078-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Priolo N, Arribére CM, Caffini N, Barberis S, Vázquez RN, Luco JM. Isolation and purification of cysteine peptidases from the latex of Araujia hortorum fruits. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1381-1177(01)00022-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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