51
|
Shi G, Dang Y, Pan T, Liu X, Liu H, Li S, Zhang L, Zhao H, Li S, Han J, Tai R, Zhu Y, Li J, Ji Q, Mole RA, Yu D, Fang H. Unexpectedly Enhanced Solubility of Aromatic Amino Acids and Peptides in an Aqueous Solution of Divalent Transition-Metal Cations. PHYSICAL REVIEW LETTERS 2016; 117:238102. [PMID: 27982649 DOI: 10.1103/physrevlett.117.238102] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 06/06/2023]
Abstract
We experimentally observed considerable solubility of tryptophan (Trp) in a CuCl_{2} aqueous solution, which could reach 2-5 times the solubility of Trp in pure water. Theoretical studies show that the strong cation-π interaction between Cu^{2+} and the aromatic ring in Trp modifies the electronic distribution of the aromatic ring to enhance significantly the water affinity of Trp. Similar solubility enhancement has also been observed for other divalent transition-metal cations (e.g., Zn^{2+} and Ni^{2+}), another aromatic amino acid (phenylalanine), and three aromatic peptides (Trp-Phe, Phe-Phe, and Trp-Ala-Phe).
Collapse
Affiliation(s)
- Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yaru Dang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tingting Pan
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xing Liu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Hui Liu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shaoxian Li
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Lijuan Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China
| | - Hongwei Zhao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shaoping Li
- School of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaguang Han
- Center for Terahertz Waves and College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Renzhong Tai
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China
| | - Yiming Zhu
- Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516, Jungong Road, 200093, Shanghai, China
| | - Jichen Li
- School of Physics and Astronomy, the University of Manchester, Manchester M13 9PL, United Kingdom
| | - Qing Ji
- Institute of Biophysics, Hebei University of Technology, Tianjin 300401, China
| | - R A Mole
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Dehong Yu
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| |
Collapse
|
52
|
Mandair GS, Han AL, Keller ET, Morris MD. Raman microscopy of bladder cancer cells expressing green fluorescent protein. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:115001. [PMID: 27805248 PMCID: PMC8357324 DOI: 10.1117/1.jbo.21.11.115001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/14/2016] [Indexed: 05/06/2023]
Abstract
Gene engineering is a commonly used tool in cellular biology to determine changes in function or expression of downstream targets. However, the impact of genetic modulation on biochemical effects is less frequently evaluated. The aim of this study is to use Raman microscopy to assess the biochemical effects of gene silencing on T24 and UMUC-13 bladder cancer cell lines. Cellular biochemical information related to nucleic acid and lipogenic components was obtained from deconvolved Raman spectra. We show that the green fluorescence protein (GFP), the chromophore that served as a fluorescent reporter for gene silencing, could also be detected by Raman microscopy. Only the gene-silenced UMUC-13 cell lines exhibited low-to-moderate GFP fluorescence as determined by fluorescence imaging and Raman spectroscopic studies. Moreover, we show that gene silencing and cell phenotype had a greater effect on nucleic acid and lipogenic components with minimal interference from GFP expression. Gene silencing was also found to perturb cellular protein secondary structure in which the amount of disorderd protein increased at the expense of more ordered protein. Overall, our study identified the spectral signature for cellular GFP expression and elucidated the effects of gene silencing on cancer cell biochemistry and protein secondary structure.
Collapse
Affiliation(s)
- Gurjit S. Mandair
- University of Michigan, School of Dentistry, Department of Biologic and Materials Sciences, 1011 North University Avenue, Ann Arbor, Michigan 48109-1078, United States
- Address all correspondence to: Gurjit S. Mandair, E-mail:
| | - Amy L. Han
- University of Michigan, Department of Urology and Biointerfaces Institute, NCRC Building 20, 2800 Plymouth Road, Ann Arbor, Michigan 48109-2800, United States
| | - Evan T. Keller
- University of Michigan, Department of Urology and Biointerfaces Institute, NCRC Building 20, 2800 Plymouth Road, Ann Arbor, Michigan 48109-2800, United States
| | - Michael D. Morris
- University of Michigan, Department of Chemistry, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
53
|
Jannone JM, Grigg JI, Aguirre LM, Jones EM. Electrostatic Interactions at N- and C-Termini Determine Fibril Polymorphism in Serum Amyloid A Fragments. J Phys Chem B 2016; 120:10258-10268. [PMID: 27632709 DOI: 10.1021/acs.jpcb.6b07672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid polymorphism presents a challenge to physical theories of amyloid formation and stability. The amyloidogenic protein serum amyloid A (SAA) exhibits complex and unexplained structural polymorphism in its N-terminal fragments: the N-terminal 11-residue peptide (SAA1-11) forms left-handed helical fibrils, while extension by one residue (SAA1-12) produces a rare right-handed amyloid. In this study, we use a combination of vibrational spectroscopy and ultramicroscopy to examine fibrils of these peptides and their terminally acetylated and amidated variants, in an effort to uncover the physical basis for this effect. Raman spectroscopy and atomic force microscopy provide evidence that SAA1-12 forms a β-helical fibril architecture, while SAA1-11 forms more typical stacked β-sheets. Importantly, N-terminal acetylation blocks fibril formation by SAA1-12 with no effect on SAA1-11, while C-terminal amidation has nearly the opposite effect. Together, these data suggest distinct electrostatic interactions at the N- and C-termini stabilize the two fibril structures; we propose model fibril structures in which C-terminal extension changes the favored intermolecular interaction between peptide monomers from an Arg1-C-terminus charge pair to an N-terminus-C-terminus charge pair. This model suggests a general mechanism for charge-mediated amyloid polymorphism and may inform strategies for design of peptide-based nanomaterials stabilized by engineered intermolecular contacts.
Collapse
Affiliation(s)
- Justine M Jannone
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
| | - James I Grigg
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
| | - Lauren M Aguirre
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
| | - Eric M Jones
- Department of Chemistry and Biochemistry, California Polytechnic State University San Luis Obispo, California 93407 United States
| |
Collapse
|
54
|
Meng L, Wu W, Lin Z. Electronic structures of intermolecular hydrogen bond contacts with solute in aqueous solution: glycine as a working prototype. Phys Chem Chem Phys 2016; 18:15894-8. [PMID: 27243041 DOI: 10.1039/c5cp07968c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The intermolecular hydrogen bond (H-bond) interactions play vital roles in many biological systems. Despite continued interest, the nature of their electronic structures has remained elusive. Based on the unique features of aqueous solution, a simple model depicting the H-bond electronic states by orbital hybridizations is developed. The model is demonstrated by reproducing the experimental IR data and yielding favorable solute-solvent interactions for the prototype glycine. The H-bond state for solute H, O and N atoms is found to be characterized by sp(1), sp(2), and sp(3) hybridizations, respectively. The model provides a new way for probing the intricate solute-solvent contacts.
Collapse
Affiliation(s)
- Lingbiao Meng
- Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900, China.
| | | | | |
Collapse
|
55
|
Badawi HM, Khan I. A comparative study of the vibrational spectra of the anticancer drug melphalan and its fundamental molecules 3-phenylpropionic acid and l-phenylalanine. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
56
|
|
57
|
Yamada D, Yamamoto J, Zhang Y, Iwata T, Hitomi K, Getzoff ED, Iwai S, Kandori H. Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase. Biochemistry 2016; 55:715-23. [PMID: 26719910 DOI: 10.1021/acs.biochem.5b01111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleotide (FAD) is the chromophore of both PHRs, and the resting oxidized form (FAD(ox)), at least under in vitro purified conditions, is first photoconverted to the neutral semiquinoid radical (FADH(•)) form, followed by photoconversion into the enzymatically active fully reduced (FADH(-)) form. Previously, we reported light-induced difference Fourier transform infrared (FTIR) spectra corresponding to the photoactivation process of Xenopus (6-4) PHR. Spectral differences between the absence and presence of (6-4) PP were observed in the photoactivation process. To identify the FTIR signals where these differences appeared, we compared the FTIR spectra of photoactivation (i) in the presence and absence of (6-4) PP, (ii) of (13)C labeling, (15)N labeling, and [(14)N]His/(15)N labeling, and (iii) of H354A and H358A mutants. We successfully assigned the vibrational bands for (6-4) PP, the α-helix and neutral His residue(s). In particular, we assigned three bands to the C ═ O groups of (6-4) PP in the three different redox states of FAD. Furthermore, the changed hydrogen bonding environments of C ═ O groups of (6-4) PP suggested restructuring of the binding pocket of the DNA lesion in the process of photoactivation.
Collapse
Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Yu Zhang
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Kenichi Hitomi
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.,Life Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
58
|
Hernández B, López-Tobar E, Sanchez-Cortes S, Coïc YM, Baron B, Chenal A, Kruglik SG, Pflüger F, Cohen R, Ghomi M. From bulk to plasmonic nanoparticle surfaces: the behavior of two potent therapeutic peptides, octreotide and pasireotide. Phys Chem Chem Phys 2016; 18:24437-50. [DOI: 10.1039/c6cp04421b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural dynamics of two potent somatostatin analogues in an aqueous environment and their binding sites on plasmonic nanoparticles were described.
Collapse
Affiliation(s)
- Belén Hernández
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
| | | | | | - Yves-Marie Coïc
- Institut Pasteur
- Unité de Chimie des Biomolécules
- UMR 3523
- 75724 Paris Cedex 15
- France
| | - Bruno Baron
- Institut Pasteur
- Plate-Forme de Biophysique de Macromolécules et de leurs Interactions
- 75724 Paris Cedex 15
- France
| | - Alexandre Chenal
- Institut Pasteur
- Unité Biochimie des Interactions Macromoléculaires
- UMR CNRS 3528
- 75724 Paris Cedex 15
- France
| | - Sergei G. Kruglik
- Sorbonne Universités
- UPMC Univ. Paris 06
- UMR 8237
- Laboratoire Jean Perrin
- 75005 Paris
| | - Fernando Pflüger
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
| | - Régis Cohen
- Service d’Endocrinologie
- Centre Hospitalier de Saint-Denis
- 93200 Saint-Denis
- France
| | - Mahmoud Ghomi
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
| |
Collapse
|
59
|
Yao G, Zhang J, Huang Q. Conformational and vibrational analyses of meta-tyrosine: An experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:111-123. [PMID: 26125991 DOI: 10.1016/j.saa.2015.06.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
M-tyrosine is one kind of positional isomer of tyrosine which is widely applied in agrichemical, medicinal chemistry, and food science. However, the structural and vibrational features of m-tyrosine have not been reported or systematically investigated. In this work, potential energy surface (PES) calculations were used for searching and determining the stable zwitterionic conformers of m-tyrosine, and the Raman spectra of m-tyrosine and deuterated m-tyrosine were measured and interpreted based on theoretical computation. For the spectral simulation, several DFT-based quantum chemistry (QC) methods were employed, and the M06-2X functional with SMD solvent model was found to be best in reproducing the Raman spectra and geometrical property. As such, this study has not only presented a detailed study of m-tyrosine's vibrational property which is lack in the literature, but also may shed some light on the optimal choice of QC methods for calculation of conformations and vibrational properties of zwitterionic amino acids.
Collapse
Affiliation(s)
- Guohua Yao
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Jingjing Zhang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Qing Huang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China; University of Science & Technology of China, Hefei, Anhui 230026, PR China.
| |
Collapse
|
60
|
Kowalska-Baron A. Theoretical study of the complexes of tyrosine and tryptophan with biologically important metal cations in aqueous solutions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
61
|
Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:473-483. [PMID: 25036456 DOI: 10.1016/j.saa.2014.06.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/13/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.
Collapse
Affiliation(s)
- Benjamin A Anderson
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Alex Literati
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Borden Ball
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Jan Kubelka
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States.
| |
Collapse
|
62
|
de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
Collapse
Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| |
Collapse
|
63
|
Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. Interaction between the guanidinium cation and aromatic amino acids. Phys Chem Chem Phys 2014; 16:22499-512. [DOI: 10.1039/c4cp02630f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
64
|
Sjöberg B, Foley S, Cardey B, Enescu M. An experimental and theoretical study of the amino acid side chain Raman bands in proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:300-11. [PMID: 24681316 DOI: 10.1016/j.saa.2014.02.080] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 05/15/2023]
Abstract
The Raman spectra of a series of tripeptides with the basic formula GlyAAGly where the central amino acid (AA) was tryptophan, tyrosine, phenylalanine, glycine, methionine, histidine, lysine and leucine were measured in H2O. The theoretical Raman spectra obtained using density functional theory (DFT) calculations at the B3LYP/6-311+G(2df,2pd) level of theory allows a precise attribution of the vibrational bands. The experimental results show that there is a blue shift in the frequencies of several bands of the amino acid side chains in tripeptides compared to free amino acids, especially in the case of AAs containing aromatic rings. On the other hand, a very good agreement was found between the Raman bands of AA residues in tripeptides and those measured on three model proteins: bovine serum albumin, β-lactoglobulin and lysozyme. The present analysis contributes to an unambiguous interpretation of the protein Raman spectra that is useful in monitoring the biological reactions involving AA side chains alteration.
Collapse
Affiliation(s)
- Béatrice Sjöberg
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France
| | - Sarah Foley
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France.
| | - Bruno Cardey
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France
| | - Mironel Enescu
- Laboratoire Chrono-Environnement, UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030 Besançon cedex, France
| |
Collapse
|
65
|
Méndez-Hurtado J, Isabel Menéndez M, López R, Ruiz-López MF. An ab initio analysis of the structure of l-tryptophan tautomers in microhydrated environments, in water and in hydrophobic solvents. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
66
|
Protonation–deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
67
|
Cormanich RA, Ducati LC, Tormena CF, Rittner R. A theoretical and experimental 1
H NMR spectroscopy study of the stereoelectronic interactions that rule the conformational energies of alanine and valine methyl ester. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rodrigo A. Cormanich
- Chemistry Institute; University of Campinas; P.O. Box 6154 13083-970 Campinas Brazil
| | - Lucas C. Ducati
- Chemistry Institute; University of São Paulo; P. O. Box 26077 05508-900 São Paulo Brazil
| | - Cláudio F. Tormena
- Chemistry Institute; University of Campinas; P.O. Box 6154 13083-970 Campinas Brazil
| | - Roberto Rittner
- Chemistry Institute; University of Campinas; P.O. Box 6154 13083-970 Campinas Brazil
| |
Collapse
|
68
|
Amaro M, Kubiak-Ossowska K, Birch DJS, Rolinski OJ. Initial stages of beta-amyloid Aβ 1-40 and Aβ 1-42 oligomerization observed using fluorescence decay and molecular dynamics analyses of tyrosine. Methods Appl Fluoresc 2013; 1:015006. [PMID: 29148438 DOI: 10.1088/2050-6120/1/1/015006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of Alzheimer's disease is associated with the aggregation of the beta-amyloid peptides Aβ1-40 and Aβ1-42. It is believed that the small oligomers formed during the early stages of the aggregation are neurotoxic and involved in the process of neurodegeneration. In this paper we use fluorescence decay measurements of beta-amyloid intrinsic fluorophore tyrosine (Tyr) and molecular dynamics (MD) simulations to study the early stages of oligomer formation for the Aβ1-40 and Aβ1-42 peptides in vitro. We demonstrate that the lifetime distributions of the amyloid fluorescence decay efficiently describe changes in the complex Tyr photophysics during the peptide aggregation and highlight the differences in aggregation performance of the two amyloids. Tyr fluorescence decay is found to be a more sensitive sensor of Aβ1-40 aggregation than Aβ1-42 aggregation. The MD simulation of the peptide aggregation is compared with the experimental data and supports a four-rotamer model of Tyr.
Collapse
Affiliation(s)
- Mariana Amaro
- Photophysics Group, Centre for Molecular Nanometrology, Department of Physics, Scottish Universities Physics Alliance, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, UK
| | | | | | | |
Collapse
|
69
|
Griffith EC, Vaida V. Ionization state of l-Phenylalanine at the Air–Water Interface. J Am Chem Soc 2013; 135:710-6. [DOI: 10.1021/ja308089n] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Elizabeth C. Griffith
- Department of Chemistry and Biochemistry
and CIRES, University of Colorado, UCB
215, Boulder, Colorado
80309, United States
| | - Veronica Vaida
- Department of Chemistry and Biochemistry
and CIRES, University of Colorado, UCB
215, Boulder, Colorado
80309, United States
| |
Collapse
|
70
|
Shimozono Y, Yamada K, Ishiuchi SI, Tsukiyama K, Fujii M. Revised conformational assignments and conformational evolution of tyrosine by laser desorption supersonic jet laser spectroscopy. Phys Chem Chem Phys 2013; 15:5163-75. [DOI: 10.1039/c3cp43573c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
71
|
Grebner C, Kästner J, Thiel W, Engels B. A New Tabu-Search-Based Algorithm for Solvation of Proteins. J Chem Theory Comput 2012; 9:814-21. [DOI: 10.1021/ct300898d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Grebner
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
| | - Johannes Kästner
- Universität
Stuttgart,
Institut für Theoretische Chemie, Pfaffenwaldring 55, D-70569
Stuttgart, Germany
| | - Walter Thiel
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an
der Ruhr, Germany
| | - Bernd Engels
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
| |
Collapse
|
72
|
Wojciechowska A, Gągor A, Wysokiński R, Trusz-Zdybek A. Synthesis, structure and properties of [Zn(l-Tyr)2(bpy)]2⋅ 3H2O·CH3OH complex: Theoretical, spectroscopic and microbiological studies. J Inorg Biochem 2012; 117:93-102. [PMID: 23078779 DOI: 10.1016/j.jinorgbio.2012.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 09/03/2012] [Accepted: 09/03/2012] [Indexed: 10/27/2022]
|
73
|
Hernández B, Coïc YM, Kruglik SG, Carelli C, Cohen R, Ghomi M. Octreotide used for probing the type-II' β-turn CD and Raman markers. J Phys Chem B 2012; 116:9337-45. [PMID: 22793173 DOI: 10.1021/jp3036428] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Octreotide, a potent somatostatin (SST) analogue, is used as an antiproliferative drug in numerous endocrine tumors. Previous NMR investigations, basically performed in DMSO, had evidenced a type-II' β-turn structure for this cyclic peptide. However, apart a few incomplete studies by circular dichroism, a systematic analysis of the structural behavior of octreotide in aqueous solution as a function of concentration and ionic strength was still lacking. Here, we report the chemical synthesis and purification of octreotide for optical spectroscopic purposes accompanied by its structural analysis. Furthermore, we have used octreotide as a short size, well-defined model compound for analyzing the CD and Raman markers of a type-II' β-turn. CD data collected in the 25-250 μM range revealed the general trend of octreotide to undergo a disordered toward ordered structural transition upon increasing concentration. Especially, the β-turn CD markers could be characterized above 50 μM by a negative band at ~202 nm flanked by a shoulder at ~218 nm. On the basis of Raman spectra recorded as a function of concentration (1-20 mM), we could assign the markers at ~1678 and ~1650 cm(-1) in the amide I region, and at ~1303, ~1288, and ~1251 cm(-1) in the amide III region, to the type-II' β-turn structure. The stability of the intermolecular antiparallel β-sheet formed in octreotide could be confirmed by the rigidity of the disulfide bridge which adopts a preferential gauche-gauche-gauche rotamer along the -Cβ-S-S-Cβ- moiety of the linked cysteines. The present analysis permits a better understanding of the differences between the structural features of SST-14 and its routinely used analogue, octreotide.
Collapse
Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France
| | | | | | | | | | | |
Collapse
|
74
|
Moreno JRA, Moreno MDMQ, Ureña FP, González JJL. Conformational preference of short aromatic amino acids from the FT-IR, FT-Raman and Far-IR spectroscopies, and quantum chemical calculations: l-phenylalanine and l-tyrosine. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.tetasy.2012.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
75
|
Hudecová J, Horníček J, Buděšínský M, Šebestík J, Šafařík M, Zhang G, Keiderling TA, Bouř P. Three types of induced tryptophan optical activity compared in model dipeptides: theory and experiment. Chemphyschem 2012; 13:2748-60. [PMID: 22706803 DOI: 10.1002/cphc.201200201] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/27/2012] [Indexed: 11/08/2022]
Abstract
The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp-containing cyclic dipeptides c-(Trp-X) (where X = Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π-π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm(-1) indicates the local χ(2) angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion-corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion-DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.
Collapse
Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
76
|
Leyton P, Brunet J, Silva V, Paipa C, Castillo MV, Brandán SA. An experimental and theoretical study of L-Tryptophan in an aqueous solution, combining two-layered ONIOM and SCRF calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 88:162-170. [PMID: 22226676 DOI: 10.1016/j.saa.2011.12.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/16/2011] [Accepted: 12/15/2011] [Indexed: 05/31/2023]
Abstract
ONIOM and SCRF calculations were performed to study the most stable theoretical structure of L-tryptophan in an aqueous solution phase and to observe the changes occurring in the structural and vibrational properties of L-tryptophan in the aqueous media. L-Tryptophan was characterized by infrared and Raman spectroscopies in the solid state and as an aqueous solution. Optimized geometries and relative stabilities for the L-tryptophan zwitterion were calculated while taking into account solvent effects using the self-consistent reaction field (SCRF) theory. The obtained results in the aqueous solution were compared with those calculated for the zwitterion in the gas phase by means of two-layered ONIOM calculations. For the complete assignments of the IR and Raman spectra of L-tryptophan in the aqueous solution phase, density functional theory (DFT) calculations were combined with Pulay's scaled quantum mechanical force field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental values. Additionally, the roles of specific and bulk contributions from solvent effects on the properties of l-tryptophan were analyzed. Furthermore, bands corresponding to the normal modes of vibration were localized and assigned, and they served as the bases for the calculations of the corresponding force constants. Significant effects on the geometrical and vibrational frequencies were found for the studied zwitterion.
Collapse
Affiliation(s)
- Patricio Leyton
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | | | | | | | | |
Collapse
|
77
|
Bai Y, Abbott NL. Enantiomeric interactions between liquid crystals and organized monolayers of tyrosine-containing dipeptides. J Am Chem Soc 2012; 134:548-58. [PMID: 22091988 PMCID: PMC3257416 DOI: 10.1021/ja2089475] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have examined the orientational ordering of nematic liquid crystals (LCs) supported on organized monolayers of dipeptides with the goal of understanding how peptide-based interfaces encode intermolecular interactions that are amplified into supramolecular ordering. By characterizing the orientations of nematic LCs (4-cyano-4'-pentylbiphenyl and TL205 (a mixture of mesogens containing cyclohexane-fluorinated biphenyls and fluorinated terphenyls)) on monolayers of l-cysteine-l-tyrosine, l-cysteine-l-phenylalanine, or l-cysteine-l-phosphotyrosine formed on crystallographically textured films of gold, we conclude that patterns of hydrogen bonds generated by the organized monolayers of dipeptides are transduced via macroscopic orientational ordering of the LCs. This conclusion is supported by the observation that the ordering exhibited by the achiral LCs is specific to the enantiomers used to form the dipeptide-based monolayers. The dominant role of the -OH group of tyrosine in dictating the patterns of hydrogen bonds that orient the LCs was also evidenced by the effects of phosphorylation of the tyrosine on the ordering of the LCs. Overall, these results reveal that crystallographic texturing of gold films can direct the formation of monolayers of dipeptides with long-range order, thus unmasking the influence of hydrogen bonding, chirality, and phosphorylation on the macroscopic orientational ordering of LCs supported on these surfaces. These results suggest new approaches based on supramolecular assembly for reporting the chemical functionality and stereochemistry of synthetic and biological peptide-based molecules displayed at surfaces.
Collapse
Affiliation(s)
- Yiqun Bai
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison WI 53705, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison WI 53705, United States
| |
Collapse
|
78
|
Bairi P, Roy B, Nandi AK. Bi-component hydrogel of perylene-3,4,9,10-tetracarboxylic potassium salt andl-tyrosine. RSC Adv 2012. [DOI: 10.1039/c1ra00506e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
79
|
Hernández B, Pflüger F, Adenier A, Nsangou M, Kruglik SG, Ghomi M. Energy maps, side chain conformational flexibility, and vibrational features of polar amino acidsL-serine andL-threonine in aqueous environment. J Chem Phys 2011; 135:055101. [DOI: 10.1063/1.3617415] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
80
|
Baek KY, Fujimura Y, Hayashi M, Lin SH, Kim SK. Density Functional Theory Study of Conformation-Dependent Properties of Neutral and Radical Cationic l-Tyrosine and l-Tryptophan. J Phys Chem A 2011; 115:9658-68. [DOI: 10.1021/jp200826z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- K. Y. Baek
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Y. Fujimura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
- Institute of Applied Chemistry, Institute of Molecular Science, Chiao-Tung University, Hsin-Chu, Taiwan
| | - M. Hayashi
- Center for Condensed Matter Sciences, National Taiwan University, Taipei, Taiwan
| | - S. H. Lin
- Institute of Applied Chemistry, Institute of Molecular Science, Chiao-Tung University, Hsin-Chu, Taiwan
- Institute of Atomic and Molecular Science, Academia Sinica, Taipei, Taiwan
| | - S. K. Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
- WCU Department of Biophysics and Chemical Biology, Seoul National University, Seoul, Korea
| |
Collapse
|
81
|
Hernández B, Pflüger F, Adenier A, Kruglik SG, Ghomi M. Side chain flexibility and protonation states of sulfur atom containing amino acids. Phys Chem Chem Phys 2011; 13:17284-94. [DOI: 10.1039/c1cp21054h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|