1
|
Jóźwiak M, Komudzińska M, Tyczyńska M, Marczak W, Jóźwiak A. Heat capacity of six glymes in N,N-dimethylformamide + water mixtures. Solvation of glymes. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
2
|
Tyunina EY, Barannikov VP, Dunaeva VV, Krasnov AV. Enthalpies of Sublimation and Solvation of Alanine-Containing Dipeptides. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s003602442204032x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
3
|
Batov DV, Antonova OA, Smirnova NL. Thermodynamics of the L-tryptophan interaction with glycerol or urea in water at ambient conditions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
4
|
Matyášek R, Řehůřková K, Berta Marošiová K, Kovařík A. Mutational Asymmetries in the SARS-CoV-2 Genome May Lead to Increased Hydrophobicity of Virus Proteins. Genes (Basel) 2021; 12:826. [PMID: 34072181 PMCID: PMC8227412 DOI: 10.3390/genes12060826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein-protein interactions, fusion of viral and cellular membranes, and virion assembly.
Collapse
Affiliation(s)
| | | | | | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic; (R.M.); (K.Ř.); (K.B.M.)
| |
Collapse
|
5
|
Datta A, Roy S. Thermodynamics of Solute–Solvent Interactions and Solubility of Some Amino Acids in Aqueous Sodium Iodide Solutions at T = 298.15 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2021. [DOI: 10.1134/s0036024421140041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
6
|
Applying Discriminant and Cluster Analyses to Separate Allergenic from Non-allergenic Proteins. OPEN CHEM 2019. [DOI: 10.1515/chem-2019-0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractAs a result of increased healthcare requirements and the introduction of genetically modified foods, the problem of allergies is becoming a growing health problem. The concept of allergies has prompted the use of new methods such as genomics and proteomics to uncover the nature of allergies. In the present study, a selection of 1400 food proteins was analysed by PLS-DA (Partial Least Square-based Discriminant Analysis) after suitable transformation of structural parameters into uniform vectors. Then, the resulting strings of different length were converted into vectors with equal length by Auto and Cross-Covariance (ACC) analysis. Hierarchical and non-hierarchical (K-means) Cluster Analysis (CA) was also performed in order to reach a certain level of separation within a small training set of plant proteins (16 allergenic and 16 non-allergenic) using a new three-dimensional descriptor based on surface protein properties in combination with amino acid hydrophobicity scales. The novelty of the approach in protein differentiation into allergenic and non-allergenic classes is described in the article.The general goal of the present study was to show the effectiveness of a traditional chemometric method for classification (PLS–DA) and the options of Cluster Analysis (CA) to separate by multivariate statistical methods allergenic from non-allergenic proteins.
Collapse
|
7
|
The effect of the side chain structures on the energy of intermolecular interactions of α-amino acids with some formamides in aqueous solutions at T = 298.15 K. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
Dunal J, Buczkowski A, Waliszewski D, Stepniak A, Palecz B. Effects of l-α-amino acids side chains on their interparticle interactions with the dissociated potassium chloride in aqueous solutions. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network. Proc Natl Acad Sci U S A 2016; 113:12946-12951. [PMID: 27803319 DOI: 10.1073/pnas.1616138113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the β-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles θ of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks-Chandler-Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to θ [Formula: see text] 90°, whereas all of the planar peptide networks of the polar and charged amino acids are hydrophilic due to θ [Formula: see text] 90°. Planar peptide networks of the charged amino acids exhibit complete-wetting behavior due to θ [Formula: see text] 0°. This computational approach for characterization of hydrophobicity can be extended to artificial planar networks of other soft matter.
Collapse
|
10
|
Smirnov VI, Badelin VG. Enthalpy characteristics of the dissolution of L-valine in water/formamide mixtures at 298.15 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416110261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Duan Y, Ba L, Gao J, Gao X, Zhu D, de Jong RM, Mink D, Kaluzna I, Lin Z. Semi-rational engineering of cytochrome CYP153A from Marinobacter aquaeolei for improved ω-hydroxylation activity towards oleic acid. Appl Microbiol Biotechnol 2016; 100:8779-88. [DOI: 10.1007/s00253-016-7634-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 04/10/2016] [Accepted: 05/14/2016] [Indexed: 12/25/2022]
|
12
|
Milić S, Bogdanović Pristov J, Mutavdžić D, Savić A, Spasić M, Spasojević I. The relationship of physicochemical properties to the antioxidative activity of free amino acids in Fenton system. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4245-4254. [PMID: 25764263 DOI: 10.1021/es5053396] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herein we compared antioxidative activities (AA) of 25 free L-amino acids (FAA) against Fenton system-mediated hydroxyl radical (HO(•)) production in aqueous solution, and examined the relation between AA and a set of physicochemical properties. The rank order according to AA was: Trp > norleucine > Phe, Leu > Ile > His >3,4-dihydroxyphenylalanine, Arg > Val > Lys, Tyr, Pro > hydroxyproline > α-aminobutyric acid > Gln, Thr, Ser > Glu, Ala, Gly, Asn, Asp. Sulfur-containing FAA generated different secondary reactive products, which were discriminated by the means of electron paramagnetic resonance spin-trapping spectroscopy. AA showed a general positive correlation with hydrophobicity. However, when taken separately, uncharged FAA exhibited strong positive correlation of AA with hydrophobicity whereas charged FAA showed negative or no significant correlation depending on the scale applied. A general strong negative correlation was found between AA and polarity. Steric parameters and hydration numbers correlated positively with AA of nonpolar side-chain FAA. In addition, a decrease of temperature which promotes hydrophobic hydration resulted in increased AA. This implies that HO(•)-provoked oxidation of FAA is strongly affected by hydrophobic hydration. Our findings are important for the understanding of oxidation processes in natural and waste waters.
Collapse
Affiliation(s)
- Sonja Milić
- †Department of Life Sciences, Institute for Multidisciplinary Research, University of Belgrade, Belgrade 11030, Serbia
| | - Jelena Bogdanović Pristov
- †Department of Life Sciences, Institute for Multidisciplinary Research, University of Belgrade, Belgrade 11030, Serbia
| | - Dragosav Mutavdžić
- †Department of Life Sciences, Institute for Multidisciplinary Research, University of Belgrade, Belgrade 11030, Serbia
| | - Aleksandar Savić
- †Department of Life Sciences, Institute for Multidisciplinary Research, University of Belgrade, Belgrade 11030, Serbia
| | - Mihajlo Spasić
- ‡Department of Physiology, Institute for Biological Research 'Siniša Stanković', University of Belgrade, Belgrade 11060, Serbia
| | - Ivan Spasojević
- †Department of Life Sciences, Institute for Multidisciplinary Research, University of Belgrade, Belgrade 11030, Serbia
| |
Collapse
|
13
|
Rao SS, Gejji SP. Molecular insights accompanying aggregation in amino acid ionic liquids. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
14
|
Tyrosine-mediated two-dimensional peptide assembly and its role as a bio-inspired catalytic scaffold. Nat Commun 2014; 5:3665. [DOI: 10.1038/ncomms4665] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 03/14/2014] [Indexed: 12/30/2022] Open
|
15
|
Mezhevoi IN, Badelin VG. Enthalpy pair coefficients of interaction for DL-valine in aqueous solutions of polyatomic alcohols at 298 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413120169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Romero CM, Oviedo CD. Effect of Temperature on The Solubility of α-Amino Acids and α,ω-Amino Acids in Water. J SOLUTION CHEM 2013. [DOI: 10.1007/s10953-013-0031-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Dagade DH, Madkar KR, Shinde SP, Barge SS. Thermodynamic studies of ionic hydration and interactions for amino acid ionic liquids in aqueous solutions at 298.15 K. J Phys Chem B 2013; 117:1031-43. [PMID: 23293839 DOI: 10.1021/jp310924m] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Amino acid ionic liquids are a special class of ionic liquids due to their unique acid-base behavior, biological significance, and applications in different fields such as templates in synthetic chemistry, stabilizers for biological macromolecules, etc. The physicochemical properties of these ionic liquids can easily be altered by making the different combinations of amino acids as anion along with possible cation modification which makes amino acid ionic liquids more suitable to understand the different kinds of molecular and ionic interactions with sufficient depth so that they can provide fruitful information for a molecular level understanding of more complicated biological processes. In this context, volumetric and osmotic coefficient measurements for aqueous solutions containing 1-ethyl-3-methylimidazolium ([Emim]) based amino acid ionic liquids of glycine, alanine, valine, leucine, and isoleucine are reported at 298.15 K. From experimental osmotic coefficient data, mean molal activity coefficients of ionic liquids were estimated and analyzed using the Debye-Hückel and Pitzer models. The hydration numbers of ionic liquids in aqueous solutions were obtained using activity data. Pitzer ion interaction parameters are estimated and compared with other electrolytes reported in the literature. The nonelectrolyte contribution to the aqueous solutions containing ionic liquids was studied by calculating the osmotic second virial coefficient through an application of the McMillan-Mayer theory of solution. It has been found that the second osmotic virial coefficient which includes volume effects correlates linearly with the Pitzer ion interaction parameter estimated independently from osmotic data as well as the hydrophobicity of ionic liquids. The enthalpy-entropy compensation effect, explained using the Starikov-Nordén model of enthalpy-entropy compensation, and partial molar entropy analysis for aqueous [Emim][Gly] solutions are made by using experimental Gibb's free energy data and literature enthalpy data. This study highlights that the hydrophobic interaction persists even in the limit of infinite dilution where the hydration effects are usually dominant, implying importance of hydrophobic hydration. Analysis of the results further shows that the hydration of amino acid ionic liquids occurs through the cooperative H-bond formation with the kosmotropic effect in contrast to the usual inorganic salts or hydrophobic salts like tetraalkylammonium halides.
Collapse
Affiliation(s)
- Dilip H Dagade
- Department of Chemistry, Shivaji University, Kolhapur 416004, India.
| | | | | | | |
Collapse
|
18
|
Kurhe DN, Dagade DH, Jadhav JP, Govindwar SP, Patil KJ. Studies of Enthalpy−Entropy Compensation, Partial Entropies, and Kirkwood−Buff Integrals for Aqueous Solutions of Glycine, l-Leucine, and Glycylglycine at 298.15 K. J Phys Chem B 2009; 113:16612-21. [DOI: 10.1021/jp9078585] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Deepti N. Kurhe
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Dilip H. Dagade
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Jyoti P. Jadhav
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Sanjay P. Govindwar
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Kesharsingh J. Patil
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| |
Collapse
|
19
|
Abstract
Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.
Collapse
Affiliation(s)
- Hans-Jörg Schneider
- Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken, Deutschland.
| |
Collapse
|
20
|
|
21
|
Methods of calculating protein hydrophobicity and their application in developing correlations to predict hydrophobic interaction chromatography retention. J Chromatogr A 2008; 1216:1838-44. [PMID: 19100553 DOI: 10.1016/j.chroma.2008.11.089] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 11/25/2008] [Accepted: 11/27/2008] [Indexed: 11/23/2022]
Abstract
Hydrophobic interaction chromatography (HIC) is a key technique for protein separation and purification. Different methodologies to estimate the hydrophobicity of a protein are reviewed, which have been related to the chromatographic behavior of proteins in HIC. These methodologies consider either knowledge of the three-dimensional structure or the amino acid composition of proteins. Despite some restrictions; they have proven to be useful in predicting protein retention time in HIC.
Collapse
|
22
|
Rossi S, Lo Nostro P, Lagi M, Ninham BW, Baglioni P. Specific Anion Effects on the Optical Rotation of α-Amino Acids. J Phys Chem B 2007; 111:10510-9. [PMID: 17691834 DOI: 10.1021/jp0721806] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Changes in optical rotation of some alpha-amino acids are induced by electrolytes. Such effects on l- and d-enantiomers of a range of amino acids are explored for sodium salts with varying anion. The amino acids studied were alanine, aspartic acid, glutamic acid, glutamine, proline, threonine, and tryptophan. The anion's polarizability in solution accounts for the change in [alpha] only for the halides. Self-association of amino acids in solution and pH changes due to the presence of the electrolytes do not account for the observed variations in optical activity. Specific interactions of anions with the chiral amino acids (Hofmeister effects) and salt-induced perturbations of the amino acid hydration shell appear to be responsible for the effects, and conformational changes in the chiral solutes due to the presence of ionic species are discussed.
Collapse
Affiliation(s)
- Simona Rossi
- Department of Chemistry and CSGI, University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino (Firenze), Italy
| | | | | | | | | |
Collapse
|
23
|
Palecz B. Enthalpic pair interaction coefficient between zwitterions of L-alpha-amino acids and urea molecule as a hydrophobicity parameter of amino acid side chains. J Am Chem Soc 2006; 127:17768-71. [PMID: 16351105 DOI: 10.1021/ja054407l] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dissolution enthalpies of L-alpha-proline, L-alpha-tyrosine, L-alpha-tryptophan, L-alpha-histidyne, L-alpha-arginine, L-alpha-lysine, L-aspartic acid, and L-alpha-glutamic acid in aqueous solutions of urea have been measured by calorimetry at a temperature of 298.15 K. The values of dissolution enthalpy were used to determine enthalpic heterogeneous pair interaction coefficients between the zwitterions of the natural amino acids and a molecule of urea in water solution. These coefficients were interpreted in terms of the hydrophobic or hydrophilic effects of the side chains of amino acids on their interactions with a polar molecule of urea in water.
Collapse
Affiliation(s)
- Bartlomiej Palecz
- Department of Physical Chemistry, University of Lodz, 90-236 Lodz, Pomorska 165, Poland.
| |
Collapse
|
24
|
Jóźwiak MŁG. Complex Formation of Crown Ethers with Cations in the Water–Organic Solvent Mixtures. Part VII. Thermodynamic of Interactions of Na+ Ion with 15-Crown-5 Ether in the Mixture of Water with N,N-Dimethylacetamide at 298.15 K. J INCL PHENOM MACRO 2004. [DOI: 10.1007/s10847-004-5081-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
25
|
|
26
|
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.
Collapse
Affiliation(s)
- Kallol M Biswas
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | | | | |
Collapse
|
27
|
Porat Y, Stepensky A, Ding FX, Naider F, Gazit E. Completely different amyloidogenic potential of nearly identical peptide fragments. Biopolymers 2003; 69:161-4. [PMID: 12767119 DOI: 10.1002/bip.10386] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yair Porat
- Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | | | | | | | | |
Collapse
|
28
|
Goto Y, Klinman JP. Binding of dioxygen to non-metal sites in proteins: exploration of the importance of binding site size versus hydrophobicity in the copper amine oxidase from Hansenula polymorpha. Biochemistry 2002; 41:13637-43. [PMID: 12427025 DOI: 10.1021/bi0204591] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper amine oxidases (CAOs) contain 2,4,5-trihydroxyphenylalanyl quinone (TPQ) and a copper ion in their active sites, catalyzing amine oxidation to aldehyde and ammonia concomitant with the reduction of molecular oxygen to hydrogen peroxide. Kinetic studies on the CAO from bovine serum (BSAO) [Su and Klinman (1999) Biochemistry 37, 12513-12525] and the recent reports on the cobalt substituted form of the enzyme from Hansenula polymorpha (HPAO) [Mills and Klinman (2000) J. Am. Chem. Soc. 122, 9897-9904, and Mills et al. (2002) Biochemistry, 41, 10577-10584] support pre-binding of molecular oxygen prior to a rate-limiting electron transfer from the reduced form of TPQ (p-aminohydroquinone form) to dioxygen. Although there is significant sequence homology between BSAO and HPAO, k(cat)/K(m)(O2) for BSAO under the optimal condition is one order of magnitude lower than that for HPAO. From a comparison of amino acid sequences for BSAO and HPAO, together with the X-ray crystal structure of HPAO, a plausible dioxygen pre-binding site has been identified that involves Y407, L425, and M634 in HPAO; the latter two residues are altered in BSAO to A490 and T695. To determine which of these residues plays a greater role in dioxygen chemistry, k(cat)/K(m)(O2) was determined in HPAO for the M634 --> T and L425 --> A mutants. The L425 --> A mutation does not alter k(cat)/K(m)(O2) to a large extent, whereas the M634 --> T decreased k(cat)/K(m)(O2) by one order of a magnitude, creating a catalyst that is similar to BSAO. A series of mutants at M634 (to F, L, and Q) were, therefore, prepared in HPAO and characterized with regard to k(cat)/K(m)(O2) as a function of pH. Structure reactivity correlations show a linear relationship of rate with side chain volume, rather than hydrophobicity, indicating that dioxygen reactivity increases with the bulk of the residue at position 634. This site also shows specificity for O2, in relation to the co-gas N2, since substitution of the inert gas N2 by either Ar or He has no effect on measured rates. In particular, He gas is expected to have little affinity for protein at 1 atmospheric pressure, implying little or no binding by N2 as well.
Collapse
Affiliation(s)
- Yoshio Goto
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | |
Collapse
|