1
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Monitoring peptide tyrosine nitration by spectroscopic methods. Amino Acids 2020; 53:517-532. [PMID: 33205301 DOI: 10.1007/s00726-020-02911-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022]
Abstract
Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer's and Parkinson's diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations. To explore the applicability to Nit, we use SERS to monitor tyrosine nitration in Met-Enkephalin, rev-Prion protein, and α-synuclein models. Useful nitration indicators were the intensity ratio of two tyrosine marker bands at 825 and 870 cm-1 and a bending vibration of the nitro group. During the SERS measurement, a conversion of nitrotyrosine to azobenzene containing peptides was observed. The interpretation of the spectra has been based on density functional theory (DFT) simulations. The CAM-B3LYP and ωB97XD functionals were found to be most suitable for modeling the measured data. The secondary structure of the α-synuclein models was monitored by electronic and vibrational circular dichroism (ECD and VCD) spectroscopies and modeled by molecular dynamics (MD) simulations. The results suggest that the nitration in these peptides has a limited effect on the secondary structure, but may trigger their aggregation.
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2
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Rogers DM, Jasim SB, Dyer NT, Auvray F, Réfrégiers M, Hirst JD. Electronic Circular Dichroism Spectroscopy of Proteins. Chem 2019. [DOI: 10.1016/j.chempr.2019.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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3
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Svilenov H, Winter G. The ReFOLD assay for protein formulation studies and prediction of protein aggregation during long-term storage. Eur J Pharm Biopharm 2019; 137:131-139. [DOI: 10.1016/j.ejpb.2019.02.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 11/28/2022]
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4
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Yue P, Peng S, Parkin S, Li T, Yu F, Long S. Peptidomimicry with C 2
-Symmetric Oligourea Derivatives of 1,2-Diaminocyclohexane and 1,2-Diphenyl-1,2-diaminoethane: Chirality and Chain Length-Dependent Conformation. ChemistrySelect 2018. [DOI: 10.1002/slct.201801900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pengyun Yue
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
| | - Siqing Peng
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
| | - Sean Parkin
- Department of Chemistry; University of Kentucky, Lexington, Kentucky; 40506 USA
| | - Tonglei Li
- Department of Industrial and Physical Pharmacy; Purdue University, West Lafayette; Indiana 47907 U.S.A
| | - Faquan Yu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
| | - Sihui Long
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
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5
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Jasim SB, Li Z, Guest EE, Hirst JD. DichroCalc: Improvements in Computing Protein Circular Dichroism Spectroscopy in the Near-Ultraviolet. J Mol Biol 2018; 430:2196-2202. [DOI: 10.1016/j.jmb.2017.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/24/2017] [Accepted: 12/10/2017] [Indexed: 12/13/2022]
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6
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Li Z, Hirst JD. Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet. Chem Sci 2017; 8:4318-4333. [PMID: 29163925 PMCID: PMC5637123 DOI: 10.1039/c7sc00586e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/23/2017] [Indexed: 11/30/2022] Open
Abstract
Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation of and insight into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures.
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Affiliation(s)
- Zhuo Li
- School of Chemistry , University of Nottingham , University Park , Nottingham NG7 2RD , UK .
| | - Jonathan D Hirst
- School of Chemistry , University of Nottingham , University Park , Nottingham NG7 2RD , UK .
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7
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Neira JL, Martínez-Rodríguez S, Hernández-Cifre JG, Cámara-Artigas A, Clemente P, Peralta S, Fernández-Moreno MÁ, Garesse R, García de la Torre J, Rizzuti B. Human COA3 Is an Oligomeric Highly Flexible Protein in Solution. Biochemistry 2016; 55:6209-6220. [PMID: 27791355 DOI: 10.1021/acs.biochem.6b00644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The assembly of the protein complex of cytochrome c oxidase (COX), which participates in the mitochondrial respiratory chain, requires a large number of accessory proteins (the so-called assembly factors). Human COX assembly factor 3 (hCOA3), also known as MITRAC12 or coiled-coil domain-containing protein 56 (CCDC56), interacts with the first subunit protein of COX to form its catalytic core and promotes its assemblage with the other units. Therefore, hCOA3 is involved in COX biogenesis in humans and can be exploited as a drug target in patients with mitochondrial dysfunctions. However, to be considered a molecular target, its structure and conformational stability must first be elucidated. We have embarked on the description of such features by using spectroscopic and hydrodynamic techniques, in aqueous solution and in the presence of detergents, together with computational methods. Our results show that hCOA3 is an oligomeric protein, forming aggregates of different molecular masses in aqueous solution. Moreover, on the basis of fluorescence and circular dichroism results, the protein has (i) its unique tryptophan partially shielded from solvent and (ii) a relatively high percentage of secondary structure. However, this structure is highly flexible and does not involve hydrogen bonding. Experiments in the presence of detergents suggest a slightly higher content of nonrigid helical structure. Theoretical results, based on studies of the primary structure of the protein, further support the idea that hCOA3 is a disordered protein. We suggest that the flexibility of hCOA3 is crucial for its interaction with other proteins to favor mitochondrial protein translocation and assembly of proteins involved in the respiratory chain.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , Elche, Alicante, Spain.,Biocomputation and Complex Systems Physics Institute , Zaragoza, Spain
| | | | | | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Paula Clemente
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Susana Peralta
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | - Rafael Garesse
- Departamento de Bioquímica-Instituto de Investigaciones Biomédicas "Alberto Sols", Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) , Madrid, Spain.,Instituto de Investigación Sanitaria, Hospital 12 de Octubre (i+12) , Madrid, Spain
| | | | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria , 87036 Rende, Italy
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8
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Neira JL, Medina-Carmona E, Hernández-Cifre JG, Montoliu-Gaya L, Cámara-Artigás A, Seffouh I, Gonnet F, Daniel R, Villegas S, de la Torre JG, Pey AL, Li F. The chondroitin sulfate/dermatan sulfate 4-O-endosulfatase from marine bacterium Vibrio sp FC509 is a dimeric species: Biophysical characterization of an endosulfatase. Biochimie 2016; 131:85-95. [PMID: 27687161 DOI: 10.1016/j.biochi.2016.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/24/2016] [Indexed: 02/07/2023]
Abstract
Sulfatases catalyze hydrolysis of sulfate groups. They have a key role in regulating the sulfation states that determine the function of several scaffold molecules. Currently, there are no studies of the conformational stability of endosulfatases. In this work, we describe the structural features and conformational stability of a 4-O-endosulfatase (EndoV) from a marine bacterium, which removes specifically the 4-O-sulfate from chondroitin sulfate/dermatan sulfate. For that purpose, we have used several biophysical techniques, namely, fluorescence, circular dichroism (CD), FTIR spectroscopy, analytical ultracentrifugation (AUC), differential scanning calorimetry (DSC), mass spectrometry (MS), dynamic light scattering (DLS) and size exclusion chromatography (SEC). The protein was a dimer with an elongated shape. EndoV acquired a native-like structure in a narrow pH range (7.0-9.0); it is within this range where the protein shows the maximum of enzymatic activity. The dimerization did not involve the presence of disulphide-bridges as suggested by AUC, SEC and DLS experiments in the presence of β-mercaptoethanol (β-ME). EndoV secondary structure is formed by a mixture of α and β-sheet topology, as judged by deconvolution of CD and FTIR spectra. Thermal and chemical denaturations showed irreversibility and the former indicates that protein did not unfold completely during heating.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain; Biocomputation and Complex Systems Physics Institute, Zaragoza, Spain.
| | | | | | - Laia Montoliu-Gaya
- Departament de Bioquímica i Biologia Molecular, Unitat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallés, Barcelona, Spain
| | - Ana Cámara-Artigás
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería, Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Ilham Seffouh
- CNRS UMR 8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Evry, France; Université Evry-Val-d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Evry, France
| | - Florence Gonnet
- CNRS UMR 8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Evry, France; Université Evry-Val-d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Evry, France
| | - Régis Daniel
- CNRS UMR 8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Evry, France; Université Evry-Val-d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Evry, France
| | - Sandra Villegas
- Departament de Bioquímica i Biologia Molecular, Unitat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallés, Barcelona, Spain
| | | | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Fuchuan Li
- National Glyco-engineering Research Center and State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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9
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UV-Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications. Biophys Rev 2016; 8:163-177. [PMID: 28510057 PMCID: PMC4884208 DOI: 10.1007/s12551-016-0197-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 11/07/2022] Open
Abstract
In Part 2 we discuss application of several different types of UV–Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.
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10
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Uporov IV, Forlemu NY, Nori R, Aleksandrov T, Sango BA, Mbote YEB, Pothuganti S, Thomasson KA. Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. Int J Mol Sci 2015; 16:21237-76. [PMID: 26370961 PMCID: PMC4613251 DOI: 10.3390/ijms160921237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/09/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023] Open
Abstract
The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.
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Affiliation(s)
- Igor V Uporov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Faculty of Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia.
| | - Neville Y Forlemu
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA.
| | - Rahul Nori
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Tsvetan Aleksandrov
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Boris A Sango
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Yvonne E Bongfen Mbote
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
- James E. Hurley College of Science & Mathematics, Oklahoma Baptist University, OBU Box 61772, 500 W. University, Shawnee, OK 74804, USA.
| | - Sandeep Pothuganti
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
| | - Kathryn A Thomasson
- Chemistry Department, University of North Dakota, 151 Cornell St. Stop 9024, Grand Forks, ND 58202, USA.
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11
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Naiyer A, Hassan MI, Islam A, Sundd M, Ahmad F. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. J Biomol Struct Dyn 2015; 33:2267-84. [PMID: 25586676 DOI: 10.1080/07391102.2014.999354] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Almost all proteins fold via a number of partially structured intermediates such as molten globule (MG) and pre-molten globule states. Understanding the structure of these intermediates at atomic level is often a challenge, as these states are observed under extreme conditions of pH, temperature, and chemical denaturants. Furthermore, several other processes such as chemical modification, site-directed mutagenesis (or point mutation), and cleavage of covalent bond of natural proteins often lead to MG like partially unfolded conformation. However, the dynamic nature of proteins in these states makes them unsuitable for most structure determination at atomic level. Intermediate states studied so far have been characterized mostly by circular dichroism, fluorescence, viscosity, dynamic light scattering measurements, dye binding, infrared techniques, molecular dynamics simulations, etc. There is a limited amount of structural data available on these intermediate states by nuclear magnetic resonance (NMR) and hence there is a need to characterize these states at the molecular level. In this review, we present characterization of equilibrium intermediates by biophysical techniques with special reference to NMR.
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Affiliation(s)
- Abdullah Naiyer
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi - 110025 , India
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12
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Gasymov OK, Abduragimov AR, Glasgow BJ. Probing tertiary structure of proteins using single Trp mutations with circular dichroism at low temperature. J Phys Chem B 2014; 118:986-95. [PMID: 24404774 PMCID: PMC3983331 DOI: 10.1021/jp4120145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Trp is the most spectroscopically
informative aromatic amino acid
of proteins. However, the near-UV circular dichroism (CD) spectrum
of Trp is complicated because the intensity and sign of 1La and 1Lb bands vary independently.
To resolve vibronic structure and gain site-specific information from
complex spectra, deconvolution was combined with cooling and site-directed
tryptophan substitution. Low temperature near-UV CD was used to probe
the local tertiary structure of a loop and α-helix in tear lipocalin.
Upon cooling, the enhancement of the intensities of the near-UV CD
was not uniform, but depends on the position of Trp in the protein
structure. The most enhanced 1Lb band was observed
for Trp at position 124 in the α-helix segment matching the
known increased conformational mobility during ligand binding. Some
aspects of the CD spectra of W28 and W130 were successfully linked
to specific rotamers of Trp previously obtained from fluorescence
lifetime measurements. The discussion was based on a framework that
the magnitude of the energy differences in local conformations governs
the changes in the CD intensities at low temperature. The Trp CD spectral
classification of Strickland was modified to facilitate the recognition
of pseudo peaks. Near-UV CD spectra harbor abundant information about
the conformation of proteins that site directed Trp CD can report.
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Affiliation(s)
- Oktay K Gasymov
- Departments of Pathology and Ophthalmology and Jules Stein Eye Institute, University California at Los Angeles , California 90095, United States
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13
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Fears KP, Clark TD, Petrovykh DY. Residue-Dependent Adsorption of Model Oligopeptides on Gold. J Am Chem Soc 2013; 135:15040-52. [DOI: 10.1021/ja404346p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Kenan P. Fears
- Division
of Chemistry, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Thomas D. Clark
- Division
of Chemistry, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Dmitri Y. Petrovykh
- Division
of Chemistry, Naval Research Laboratory, Washington, D.C. 20375, United States
- Department
of Physics, University of Maryland, College Park, Maryland 20742, United States
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14
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Ramos M, Araújo E, Jucá T, Monteiro-Moreira A, Vasconcelos I, Moreira R, Viana C, Beltramini L, Pereira D, Moreno F. New insights into the complex mixture of latex cysteine peptidases in Calotropis procera. Int J Biol Macromol 2013; 58:211-9. [DOI: 10.1016/j.ijbiomac.2013.04.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 04/01/2013] [Accepted: 04/03/2013] [Indexed: 11/27/2022]
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15
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Gasymov OK, Abduragimov AR, Glasgow BJ. Cation-π interactions in lipocalins: structural and functional implications. Biochemistry 2012; 51:2991-3002. [PMID: 22439821 DOI: 10.1021/bi3002902] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cation-π interaction impacts protein folding, structural stability, specificity, and molecular recognition. Cation-π interactions have been overlooked in the lipocalin family. To fill this gap, these interactions were analyzed in the 113 crystal and solution structures from the lipocalin family. The cation-π interactions link previously identified structurally conserved regions and reveal new motifs, which are beyond the reach of a sequence alignment algorithm. Functional and structural significance of the interactions were tested experimentally in human tear lipocalin (TL). TL, a prominent and promiscuous lipocalin, has a key role in lipid binding at the ocular surface. Ligand binding modulation through the loop AB at the "open" end of the barrel has been erroneously attributed solely to electrostatic interactions. Data revealed that the interloop cation-π interaction in the pair Phe28-Lys108 contributes significantly to stabilize the holo-conformation of the loop AB. Numerous energetically significant and conserved cation-π interactions were uncovered in TL and throughout the lipocalin family. Cation-π interactions, such as the highly conserved Trp17-Arg118 pair in TL, were educed in low temperature experiments of mutants with Trp to Tyr substitutions.
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Affiliation(s)
- Oktay K Gasymov
- Department of Pathology and Jules Stein Eye Institute, University California at Los Angeles, California 90095, USA.
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16
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Individual contributions of the aromatic chromophores to the near-UV Circular Dichroism in class A β-lactamases: A comparative computational analysis. Biophys Chem 2010; 151:39-45. [DOI: 10.1016/j.bpc.2010.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 05/06/2010] [Accepted: 05/08/2010] [Indexed: 11/20/2022]
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17
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Karabencheva T, Christov C. Mechanisms of protein circular dichroism: insights from computational modeling. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 80:85-115. [DOI: 10.1016/b978-0-12-381264-3.00003-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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18
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Georgakopoulou S, Möller D, Sachs N, Herrmann H, Aebi U. Near-UV circular dichroism reveals structural transitions of vimentin subunits during intermediate filament assembly. J Mol Biol 2008; 386:544-53. [PMID: 19136013 DOI: 10.1016/j.jmb.2008.12.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 12/19/2008] [Accepted: 12/19/2008] [Indexed: 10/21/2022]
Abstract
In vitro assembly of vimentin intermediate filaments (IFs) proceeds from soluble, reconstituted tetrameric complexes to mature filaments in three distinct stages: (1) within the first seconds after initiation of assembly, tetramers laterally associate into unit-length filaments (ULFs), on average 17 nm wide; (2) for the next few minutes, ULFs grow by longitudinal annealing into short, immature filaments; (3) almost concomitant with elongation, these immature filaments begin to radially compact, yielding approximately 11-nm-wide IFs at around 15 min. The near-UV CD signal of soluble tetramers exhibits two main peaks at 285 and 278 nm, which do not change during ULF formation. In contrast, the CD signal of mature IFs exhibits two major changes: (1) the 278-nm band, denoting the transition of the tyrosines from the ground state to the first vibrational mode of the excited state, is lost; (2) a red-shifted band appears at 291 nm, indicating the emergence of a new electronic species. These changes take place independently and at different time scales. The 278-nm signal disappears within the first minute of assembly, compatible with increased rigidity of the tyrosines during elongation of the ULFs. The rise of the 291-nm band has a lifetime of approximately 13 min and denotes the generation of phenolates by deprotonation of the tyrosines' hydroxyl group after they relocalize into a negatively charged environment. The appearance of such tyrosine-binding "pockets" in the assembling filaments highlights an essential part of the molecular rearrangements characterizing the later stages of the assembly process, including the radial compaction.
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Affiliation(s)
- Sofia Georgakopoulou
- M. E. Müller Institute for Structural Biology, University of Basel, Switzerland.
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Christov CZ, Karabencheva TG, Lodola A. Relationship between chiroptical properties, structural changes and interactions in enzymes: A computational study on β-lactamases from class A. Comput Biol Chem 2008; 32:167-75. [DOI: 10.1016/j.compbiolchem.2008.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/06/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
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20
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Christov C, Karabencheva T, Lodola A. Aromatic interactions and rotational strengths within protein environment: An electronic structural study on β-lactamases from class A. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Cowieson NP, King G, Cookson D, Ross I, Huber T, Hume DA, Kobe B, Martin JL. Cortactin adopts a globular conformation and bundles actin into sheets. J Biol Chem 2008; 283:16187-93. [PMID: 18375393 DOI: 10.1074/jbc.m708917200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cortactin is a filamentous actin-binding protein that plays a pivotal role in translating environmental signals into coordinated rearrangement of the cytoskeleton. The dynamic reorganization of actin in the cytoskeleton drives processes including changes in cell morphology, cell migration, and phagocytosis. In general, structural proteins of the cytoskeleton bind in the N-terminal region of cortactin and regulatory proteins in the C-terminal region. Previous structural studies have reported an extended conformation for cortactin. It is therefore unclear how cortactin facilitates cross-talk between structural proteins and their regulators. In the study presented here, circular dichroism, chemical cross-linking, and small angle x-ray scattering are used to demonstrate that cortactin adopts a globular conformation, thereby bringing distant parts of the molecule into close proximity. In addition, the actin bundling activity of cortactin is characterized, showing that fully polymerized actin filaments are bundled into sheet-like structures. We present a low resolution structure that suggests how the various domains of cortactin interact to coordinate its array of binding partners at sites of actin branching.
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Affiliation(s)
- Nathan P Cowieson
- Institute for Molecular Bioscience and Australian Research Council (ARC) Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane QLD 4072 Australia
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22
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Cowieson NP, Miles AJ, Robin G, Forwood JK, Kobe B, Martin JL, Wallace BA. Evaluating protein:protein complex formation using synchrotron radiation circular dichroism spectroscopy. Proteins 2007; 70:1142-6. [PMID: 17894344 DOI: 10.1002/prot.21631] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Circular dichroism (CD) spectroscopy beamlines at synchrotrons produce dramatically higher light flux than conventional CD instruments. This property of synchrotron radiation circular dichroism (SRCD) results in improved signal-to-noise ratios and allows data collection to lower wavelengths, characteristics that have led to the development of novel SRCD applications. Here we describe the use of SRCD to study protein complex formation, specifically evaluating the complex formed between carboxypeptidase A and its protein inhibitor latexin. Crystal structure analyses of this complex and the individual proteins reveal only minor changes in secondary structure of either protein upon complex formation (i.e., it involves only rigid body interactions). Conventional CD spectroscopy reports on changes in secondary structure and would therefore not be expected to be sensitive to such interactions. However, in this study we have shown that SRCD can identify differences in the vacuum ultraviolet CD spectra that are significant and attributable to complex formation.
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Affiliation(s)
- Nathan P Cowieson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
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23
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Carlson KL, Lowe SL, Hoffmann MR, Thomasson KA. Theoretical UV Circular Dichroism of Cyclo(l-Proline-l-Proline). J Phys Chem A 2006; 110:1925-33. [PMID: 16451026 DOI: 10.1021/jp052924k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MP2, DFT, and molecular mechanics (AMBER, CVFF, and CFF91) geometry optimizations were performed on the cyclic dipeptide cyclo(L-Pro-L-Pro) starting from crystal structure data. Three stable conformations were identified as energy minima by all methods, but assignment of relative energy varied between the methods. The pi-pi transition feature of the UV circular dichroic (CD) spectrum was predicted for each minimized structure using the classical physics method of the dipole interaction model. The model was sensitive to the different conformations. The UV-CD predictions were compared individually and as a Boltzmann-weighted composite with published experimental CD spectra [Bowman, R. L.; Kellerman, M.; Johnson, W. C., Jr. Biopolymers 1983, 22, 1045]. For all structures, the original parameters of Applequist [Applequist, J. J. Chem. Phys. 1979, 71, 4324] with a bandwidth of 3000 cm(-1) most accurately replicated experiment, except for the CFF91 structures, which matched experiment best with a bandwidth of 4000 cm(-1). The inclusion of solvent by a continuum model did not significantly alter the minimized geometries obtained by molecular or quantum mechanics, but it did have an effect on the relative predicted energies of CFF91 and B3LYP conformations. The overall effect of solvent inclusion was negligible when Boltzmann-weighted spectra were considered. Gas-phase CFF91 structures were also reasonably good for prediction of CD spectra, and when water was included via a continuum model for energy calculations, the weighting scheme resembled that of the higher-level weightings. The CD calculated using the MP2/6-311G structures and energies for weighting were most descriptive of the 180 nm negative band in the experimental CD, but red-shifted the location of the 205 nm band. DFT structures were comparably, though not identically, as descriptive of the first pi-pi band, and did a better job with placement of the second (positive) pi-pi band. DFT calculations were less sensitive to basis set effect than the MP2 calculations, with 6-31G results in close agreement with 6-311G. The results suggest that it is possible to use geometries obtained from a variety of different methods (molecular mechanical or quantum mechanical) with the classical physics dipole interaction model to qualitatively reproduce the UV CD of model amides.
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Affiliation(s)
- Kristine L Carlson
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202-9024, USA
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24
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Trindade MB, Lopes JLS, Soares-Costa A, Monteiro-Moreira AC, Moreira RA, Oliva MLV, Beltramini LM. Structural characterization of novel chitin-binding lectins from the genus Artocarpus and their antifungal activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:146-52. [PMID: 16257591 DOI: 10.1016/j.bbapap.2005.09.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 09/16/2005] [Accepted: 09/22/2005] [Indexed: 10/25/2022]
Abstract
Two novel chitin-binding lectins from seeds of Artocarpus genus were described in this paper, one from A. integrifolia (jackfruit) and one from A. incisa (breadfruit). They were purified from saline crude extract of seeds using affinity chromatography on chitin column, size-exclusion chromatography and reverse-phase chromatography on the C-18 column. Both are 14 kDa proteins, made up of 3 chains linked by disulfide bonds. The partial amino acid sequences of the two lectins showed they are homologous to each other but not to other plant chitin-binding proteins. Thus, they cannot be classified in any known plant chitin-binding protein family, particularly because of their inter-chain covalent bonds. Their circular dichroism spectra and deconvolution showed a secondary structure content of beta-sheet and unordered elements. The lectins were thermally stable until 80 degrees C and structural changes were observed below pH 6. Both lectins inhibited the growth of Fusarium moniliforme and Saccharomyces cerevisiae, and presented hemagglutination activity against human and rabbit erythrocytes. These lectins were denoted jackin (from jackfruit) and frutackin (from breadfruit).
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Affiliation(s)
- Melissa B Trindade
- Institute of Physics of São Carlos, University of São Paulo, São Paulo, Brazil
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25
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Araújo APU, Hansen D, Vieira DF, Oliveira C, Santana LA, Beltramini LM, Sampaio CAM, Sampaio MU, Oliva MLV. Kunitz-type Bauhinia bauhinioides inhibitors devoid of disulfide bridges: isolation of the cDNAs, heterologous expression and structural studies. Biol Chem 2005; 386:561-8. [PMID: 16006243 DOI: 10.1515/bc.2005.066] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Bauhinia bauhinoides cruzipain inhibitor (BbCI) and Bauhinia bauhinioides kallikrein inhibitor (BbKI) are cysteine and serine proteinase inhibitors structurally homologous to plant Kunitz-type inhibitors, but are devoid of disulfide bridges. Based on cDNA sequences, we found that BbKI and BbCI are initially synthesized as a prepropeptide comprising an N-terminal signal peptide (19 residues), the mature protein (164 residues) and a C-terminal targeting peptide (10 residues). Partial cDNAs encoding the mature enzymes plus N-terminal His-tags and thrombin cleavage sites were expressed in E. coli and the soluble proteins were purified by one-step nickel affinity chromatography. After thrombin cleavage, both proteins exhibited potent inhibitory activities toward their cognate proteinases like the wild-type proteins. BbCI inhibits human neutrophil elastase ( K i(app) 5.3 nM), porcine pancreatic elastase ( K i(app) 40 nM), cathepsin G ( K i(app) 160 nM) and the cysteine proteinases cruzipain ( K i(app) 1.2 nM), cruzain ( K i(app) 0.3 nM) and cathepsin L ( K i(app) 2.2 nM), while BbKI strongly inhibits plasma kallikrein ( K i(app) 2.4 nM) and plasmin ( K i(app) 33 nM). Circular dichroism spectra of BbCI and BbKI were in agreement with the beta-trefoil fold described for Kunitz inhibitors. The inhibitory potency of both BbCI- and BbKI-type inhibitors suggests that other, non-covalent interactions may compensate for the lack of disulfide bridges.
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Affiliation(s)
- Ana Paula Ulian Araújo
- Instituto de Física de São Carlos, Universidade Federal de São Paulo, Avenida Trabalhador Sãocarlense 400, 13560-970 São Carlos, SP, Brazil
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26
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Kelly SM, Jess TJ, Price NC. How to study proteins by circular dichroism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1751:119-39. [PMID: 16027053 DOI: 10.1016/j.bbapap.2005.06.005] [Citation(s) in RCA: 2282] [Impact Index Per Article: 120.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 06/08/2005] [Accepted: 06/08/2005] [Indexed: 11/30/2022]
Abstract
Circular dichroism (CD) is being increasingly recognised as a valuable technique for examining the structure of proteins in solution. However, the value of many studies using CD is compromised either by inappropriate experimental design or by lack of attention to key aspects of instrument calibration or sample characterisation. In this article, we summarise the basis of the CD approach and its application to the study of proteins, and then present clear guidelines on how reliable data can be obtained and analysed.
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Affiliation(s)
- Sharon M Kelly
- Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
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Carlson KL, Lowe SL, Hoffmann MR, Thomasson KA. Theoretical UV Circular Dichroism of Aliphatic Cyclic Dipeptides. J Phys Chem A 2005; 109:5463-70. [PMID: 16839074 DOI: 10.1021/jp046580u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four cyclic dipeptides (piperazine-2,5-diones), cyclo(L-Pro-Gly), cyclo(L-Pro-L-Leu), cyclo(L-Ala-L-Ala), and cyclo(L-Pro-L-Ala), were modeled from crystal structure data. Conformations resulting from energy minimization using molecular mechanics were compared with traditional ab initio and density functional theory geometric optimizations for each dipeptide. In all computational cases, the gas phase was assumed. The pi-pi transition feature of the UV circular dichroic (CD) spectra was predicted for each peptide structure via the classical dipole interaction model. The dipole interaction model predicted CD spectra that qualitatively agreed with experiment when MP2 or DFT geometries were used. By coupling MP2 or DFT geometric optimizations with the classical physics method of the dipole interaction model, significantly better CD spectra were calculated than those using geometries obtained by molecular mechanics. Thus, one can couple quantum mechanical geometries with a classical physics model for calculation of circular dichroism.
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Affiliation(s)
- Kristine L Carlson
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202-9024, USA
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28
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Christov C, Kantardjiev A, Karabencheva T, Tielens F. Mechanisms of generation of the rotational strengths in TEM-1 β-lactamase. Part II: theoretical study of the effects of the electrostatic interactions in the near-UV. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Comparative theoretical study of the mechanisms of generation of rotational strengths in the near-UV in β-lactamases from class A. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.09.099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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