메뉴 건너뛰기




Volumn 42, Issue 5, 2016, Pages 398-404

Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

Author keywords

alanine polypeptides; chain length; conformation; hydrogen bond; molecular dynamics; Terahertz spectra

Indexed keywords

AMINO ACIDS; CHAIN LENGTH; CONFORMATIONS; ELECTROMAGNETIC WAVE ABSORPTION; HYDROGEN BONDS; MOLECULES; WATER ABSORPTION;

EID: 84945450343     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2015.1059429     Document Type: Article
Times cited : (18)

References (49)
  • 2
    • 84874966695 scopus 로고    scopus 로고
    • Identification of biomolecules by terahertz spectroscopy and fuzzy pattern recognition
    • Chen T, Li Z, Mo W. Identification of biomolecules by terahertz spectroscopy and fuzzy pattern recognition. Acta Pt A-Molec Biomol Spectr. 2013; 106: 48-53. doi: 10.1016/j.saa.2012.12.096.
    • (2013) Acta Pt A-Molec Biomol Spectr , vol.106 , pp. 48-53
    • Chen, T.1    Li, Z.2    Mo, W.3
  • 3
    • 57649181768 scopus 로고    scopus 로고
    • A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis
    • Zhang HL, Zukowski E, Balu R, Gregurick SK. A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis. J Mol Graph. 2009; 27 (5): 655-663. doi: 10.1016/j.jmgm.2008.10.005.
    • (2009) J Mol Graph , vol.27 , Issue.5 , pp. 655-663
    • Zhang, H.L.1    Zukowski, E.2    Balu, R.3    Gregurick, S.K.4
  • 6
    • 0034821115 scopus 로고    scopus 로고
    • The interaction between terahertz radiation and biological tissue
    • Smye SW, Chamberlain JM, Fitzgerald AJ, Berry E. The interaction between terahertz radiation and biological tissue. Phys Med Biol. 2001; 46 (9): R101-R112. doi: 10.1088/0031-9155/46/9/201
    • (2001) Phys Med Biol , vol.46 , Issue.9 , pp. R101-R112
    • Smye, S.W.1    Chamberlain, J.M.2    Fitzgerald, A.J.3    Berry, E.4
  • 7
    • 0037038534 scopus 로고    scopus 로고
    • Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy
    • Fischer BM, Walther M, Jepsen PU. Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy. Phys Med Biol. 2002; 47 (21): 3807-3814. doi: 10.1088/0031-9155/47/21/319.
    • (2002) Phys Med Biol , vol.47 , Issue.21 , pp. 3807-3814
    • Fischer, B.M.1    Walther, M.2    Jepsen, P.U.3
  • 8
    • 0037425083 scopus 로고    scopus 로고
    • Temperature-dependent low-frequency vibrational spectra of purine and adenine
    • Shen YC, Upadhya PC, Linfield EH, Davies AG. Temperature-dependent low-frequency vibrational spectra of purine and adenine. Appl Phys Lett. 2003; 82 (14): 2350-2352. doi: 10.1063/1.1565680.
    • (2003) Appl Phys Lett , vol.82 , Issue.14 , pp. 2350-2352
    • Shen, Y.C.1    Upadhya, P.C.2    Linfield, E.H.3    Davies, A.G.4
  • 9
    • 24144457578 scopus 로고    scopus 로고
    • Observation of far-infrared emission from excited cytosine molecules
    • Shen YC, Upadhya PC, Linfield EH, Davies AG. Observation of far-infrared emission from excited cytosine molecules. Appl Phys Lett. 2005; 87 (1): 011105. doi: 10.1063/1.1968412.
    • (2005) Appl Phys Lett , vol.87 , Issue.1 , pp. 011105
    • Shen, Y.C.1    Upadhya, P.C.2    Linfield, E.H.3    Davies, A.G.4
  • 10
    • 84861100399 scopus 로고    scopus 로고
    • Far-infrared spectroscopy analysis of linear and cyclic peptides, and lysozyme
    • Ding T, Middelberg APJ, Huber T, Falconer RJ. Far-infrared spectroscopy analysis of linear and cyclic peptides, and lysozyme. Vib Spectrosc. 2012; 61: 144-150. doi: 10.1016/j.vibspec.2012.02.020.
    • (2012) Vib Spectrosc , vol.61 , pp. 144-150
    • Ding, T.1    Middelberg, A.P.J.2    Huber, T.3    Falconer, R.J.4
  • 11
    • 80054903227 scopus 로고    scopus 로고
    • Characterization of low-frequency modes in aqueous peptides using far-infrared spectroscopy and molecular dynamics simulation
    • Ding T, Huber T, Middelberg APJ, Falconer RJ. Characterization of low-frequency modes in aqueous peptides using far-infrared spectroscopy and molecular dynamics simulation. J Phys Chem A. 2011; 115 (42): 11559-11565. doi: 10.1021/jp200553d.
    • (2011) J Phys Chem A , vol.115 , Issue.42 , pp. 11559-11565
    • Ding, T.1    Huber, T.2    Middelberg, A.P.J.3    Falconer, R.J.4
  • 13
    • 0001894533 scopus 로고    scopus 로고
    • Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz
    • Markelz AG, Roitberg A, Heilweil EJ. Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz. Chem Phys Lett. 2000; 320 (1-2): 42-48. doi: 10.1016/S0009-2614(00)00227-X
    • (2000) Chem Phys Lett , vol.320 , Issue.1-2 , pp. 42-48
    • Markelz, A.G.1    Roitberg, A.2    Heilweil, E.J.3
  • 15
    • 0344271783 scopus 로고    scopus 로고
    • A functionalized THz sensor for marker-free DNA analysis
    • Nagel M, Richter F, Haring-bolívar P, Kurz H. A functionalized THz sensor for marker-free DNA analysis. Phys Med Biol. 2003; 48 (22): 3625-3636. doi: 10.1088/0031-9155/48/22/001.
    • (2003) Phys Med Biol , vol.48 , Issue.22 , pp. 3625-3636
    • Nagel, M.1    Richter, F.2    Haring-Bolívar, P.3    Kurz, H.4
  • 16
    • 41349089013 scopus 로고    scopus 로고
    • Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy
    • Castro-Camus E, Johnston MB. Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy. Chem Phys Lett. 2008; 455 (4-6): 289-292. doi: 10.1016/j.cplett.2008.02.084.
    • (2008) Chem Phys Lett , vol.455 , Issue.4-6 , pp. 289-292
    • Castro-Camus, E.1    Johnston, M.B.2
  • 17
    • 7444225232 scopus 로고    scopus 로고
    • Label-free amplified bioaffinity detection using terahertz wave technology
    • Menikh A, Mickan SP, Liu HB, MacColl R, Zhang XC. Label-free amplified bioaffinity detection using terahertz wave technology. Biosens Bioelectron. 2004; 20 (3): 658-662. doi: 10.1016/j.bios.2004.03.006.
    • (2004) Biosens Bioelectron , vol.20 , Issue.3 , pp. 658-662
    • Menikh, A.1    Mickan, S.P.2    Liu, H.B.3    MacColl, R.4    Zhang, X.C.5
  • 18
    • 79953101256 scopus 로고    scopus 로고
    • Protein association investigated by THz spectroscopy and molecular modeling, Laser Applications in Life Sciences 2010
    • Mernea M, Calborean O, Petrescu L, Tita A, Leca A, Dascalu T, Mihailescu DF. Protein association investigated by THz spectroscopy and molecular modeling, Laser Applications in Life Sciences 2010. Proc SPIE-Int Soc Opt Eng. 2010; 7376: 73760-73769.
    • (2010) Proc SPIE-Int Soc Opt Eng , vol.7376 , pp. 73760-73769
    • Mernea, M.1    Calborean, O.2    Petrescu, L.3    Tita, A.4    Leca, A.5    Dascalu, T.6    Mihailescu, D.F.7
  • 19
    • 84862244780 scopus 로고    scopus 로고
    • Experimental and theoretical investigations on the terahertz vibrational spectroscopy of alanine crystal
    • Wang G, Wang WN. Experimental and theoretical investigations on the terahertz vibrational spectroscopy of alanine crystal. Acta Physico-Chimica Sinica. 2012; 28: 1579-1585.
    • (2012) Acta Physico-Chimica Sinica , vol.28 , pp. 1579-1585
    • Wang, G.1    Wang, W.N.2
  • 20
    • 84863874917 scopus 로고    scopus 로고
    • First principles investigation of l-alanine in terahertz region
    • Zheng ZP, Fan WH. First principles investigation of l-alanine in terahertz region. J Biol Phys. 2012; 38 (3): 405-413. doi: 10.1007/s10867-012-9261-0.
    • (2012) J Biol Phys , vol.38 , Issue.3 , pp. 405-413
    • Zheng, Z.P.1    Fan, W.H.2
  • 21
    • 84888585161 scopus 로고    scopus 로고
    • Analysis of vibrational spectra of solid-state adenine and adenosine in the terahertz region
    • Zhang F, Kambara O, Tominaga K, Nishizawa J, Sasaki T, Wang HW, Hayashi M. Analysis of vibrational spectra of solid-state adenine and adenosine in the terahertz region. Rsc Adv. 2014; 4 (1): 269-278. doi: 10.1039/C3RA44285C.
    • (2014) Rsc Adv , vol.4 , Issue.1 , pp. 269-278
    • Zhang, F.1    Kambara, O.2    Tominaga, K.3    Nishizawa, J.4    Sasaki, T.5    Wang, H.W.6    Hayashi, M.7
  • 22
    • 57449110776 scopus 로고    scopus 로고
    • Terahertz absorption of DNA decamer duplex
    • Li XW, Globus T, Gelmont B, Salay LC, Bykhovski A. Terahertz absorption of DNA decamer duplex. J Phys Chem A. 2008; 112 (47): 12090-12096. doi: 10.1021/jp806630w.
    • (2008) J Phys Chem A , vol.112 , Issue.47 , pp. 12090-12096
    • Li, X.W.1    Globus, T.2    Gelmont, B.3    Salay, L.C.4    Bykhovski, A.5
  • 25
    • 77955509168 scopus 로고    scopus 로고
    • Low-frequency spectra of amino acids and short-chain peptides studied by terahertz time-domain spectroscopy
    • Ponseca CS, Kambara O, Kawaguchi S, Yamamoto K, Tominaga K. Low-frequency spectra of amino acids and short-chain peptides studied by terahertz time-domain spectroscopy. J Infrared Millim Terahertz Waves. 2010; 31 (7): 799-809. doi: 10.1007/s10762-010-9636-x.
    • (2010) J Infrared Millim Terahertz Waves , vol.31 , Issue.7 , pp. 799-809
    • Ponseca, C.S.1    Kambara, O.2    Kawaguchi, S.3    Yamamoto, K.4    Tominaga, K.5
  • 26
    • 58849149479 scopus 로고    scopus 로고
    • Terahertz spectra and normal mode analysis of the crystalline VA class dipeptide nanotubes
    • Zhang H, Siegrist K, Plusquellic DF, Gregurick SK. Terahertz spectra and normal mode analysis of the crystalline VA class dipeptide nanotubes. J Am Chem Soc. 2008; 130 (52): 17846-17857. doi: 10.1021/ja805581n.
    • (2008) J Am Chem Soc , vol.130 , Issue.52 , pp. 17846-17857
    • Zhang, H.1    Siegrist, K.2    Plusquellic, D.F.3    Gregurick, S.K.4
  • 27
    • 60749086203 scopus 로고    scopus 로고
    • Normal mode analysis for proteins
    • Skjaerven L, Hollup SM, Reuter N. Normal mode analysis for proteins. J Mol Struc-Theochem. 2009; 898 (1-3): 42-48. doi: 10.1016/j.theochem.2008.09.024.
    • (2009) J Mol Struc-Theochem , vol.898 , Issue.1-3 , pp. 42-48
    • Skjaerven, L.1    Hollup, S.M.2    Reuter, N.3
  • 28
    • 84903362480 scopus 로고    scopus 로고
    • Molecular dynamics study of the pressure-dependent terahertz infrared absorption spectrum of α-and γ-rdx
    • Pereverzev A, Sewell TD, Thompson DL. Molecular dynamics study of the pressure-dependent terahertz infrared absorption spectrum of α-and γ-rdx. J Chem Phys. 2013; 139 (4): 044108. doi: 10.1063/1.4813795.
    • (2013) J Chem Phys , vol.139 , Issue.4 , pp. 044108
    • Pereverzev, A.1    Sewell, T.D.2    Thompson, D.L.3
  • 29
    • 0030004479 scopus 로고    scopus 로고
    • Structural fluctuations of myoglobin from normal-modes Mossbauer Raman and absorption spectroscopy
    • Melchers B, Knapp EW, Parak F, Cordone L, Cupane A, Leone M. Structural fluctuations of myoglobin from normal-modes Mossbauer, Raman, and absorption spectroscopy. Biophys J. 1996; 70: 2092-2099.
    • (1996) Biophys J , vol.70 , pp. 2092-2099
    • Melchers, B.1    Knapp, E.W.2    Parak, F.3    Cordone, L.4    Cupane, A.5    Leone, M.6
  • 30
    • 0042769222 scopus 로고    scopus 로고
    • Normal-mode analysis without the Hessian: A driven molecular-dynamics approach
    • Bowman JM, Zhang XB, Brown A. Normal-mode analysis without the Hessian: a driven molecular-dynamics approach. J Chem Phys. 2003; 119 (2): 646-650. doi: 10.1063/1.1578475.
    • (2003) J Chem Phys , vol.119 , Issue.2 , pp. 646-650
    • Bowman, J.M.1    Zhang, X.B.2    Brown, A.3
  • 31
    • 79960161818 scopus 로고    scopus 로고
    • Terahertz spectrum and normal-mode relaxation in pentaerythritol tetranitrate: Effect of changes in bond-stretching force-field terms
    • Pereverzev A, Sewell TD. Terahertz spectrum and normal-mode relaxation in pentaerythritol tetranitrate: effect of changes in bond-stretching force-field terms. J Chem Phys. 2011; 134 (24): 244502. doi: 10.1063/1.3600756.
    • (2011) J Chem Phys , vol.134 , Issue.24 , pp. 244502
    • Pereverzev, A.1    Sewell, T.D.2
  • 32
    • 0942277699 scopus 로고    scopus 로고
    • Normal modes and frequencies from covariances in molecular dynamics or Monte Carlo simulations
    • Strachan A. Normal modes and frequencies from covariances in molecular dynamics or Monte Carlo simulations. J Chem Phys. 2004; 120 (1): 1-4. doi: 10.1063/1.1635364.
    • (2004) J Chem Phys , vol.120 , Issue.1 , pp. 1-4
    • Strachan, A.1
  • 33
    • 34250853492 scopus 로고    scopus 로고
    • Estimating the configurational entropy from molecular dynamics simulations: Anharmonicity and correlation corrections to the quasi-harmonic approximation
    • Baron R, van Gunsteren WF, Hünenberger PH. Estimating the configurational entropy from molecular dynamics simulations: anharmonicity and correlation corrections to the quasi-harmonic approximation. Trends Phys Chem. 2006; 11: 87-122.
    • (2006) Trends Phys Chem , vol.11 , pp. 87-122
    • Baron, R.1    Van Gunsteren, W.F.2    Hünenberger, P.H.3
  • 34
    • 0000961995 scopus 로고
    • Evaluation of the configurational entropy for proteins: Application to molecular dynamics simulations of an α-helix
    • Levy RM, Karplus M, Kushick J, Perahia D. Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix. Macromolecules. 1984; 17 (7): 1370-1374. doi: 10.1021/ma00137a013.
    • (1984) Macromolecules , vol.17 , Issue.7 , pp. 1370-1374
    • Levy, R.M.1    Karplus, M.2    Kushick, J.3    Perahia, D.4
  • 35
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M, Kushick JN. Method for estimating the configurational entropy of macromolecules. Macromolecules. 1981; 14 (2): 325-332. doi: 10.1021/ma50003a019.
    • (1981) Macromolecules , vol.14 , Issue.2 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 36
    • 0038613589 scopus 로고    scopus 로고
    • Sub-millimetre wave absorption spectra of artificial RNA molecules
    • Globus T, Bykhovskaia M, Woolard D, Gelmont B. Sub-millimetre wave absorption spectra of artificial RNA molecules. J Phys D Appl Phys. 2003; 36 (11): 1314-1322. doi: 10.1088/0022-3727/36/11/312.
    • (2003) J Phys D Appl Phys , vol.36 , Issue.11 , pp. 1314-1322
    • Globus, T.1    Bykhovskaia, M.2    Woolard, D.3    Gelmont, B.4
  • 39
    • 78651339654 scopus 로고    scopus 로고
    • Terahertz normal mode relaxation in pentaerythritol tetranitrate
    • Pereverzev A, Sewell TD. Terahertz normal mode relaxation in pentaerythritol tetranitrate. J Chem Phys. 2011; 134 (1): 014513. doi: 10.1063/1.3518423.
    • (2011) J Chem Phys , vol.134 , Issue.1 , pp. 014513
    • Pereverzev, A.1    Sewell, T.D.2
  • 41
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 2006; 65 (3): 712-725. doi: 10.1002/prot.21123.
    • (2006) Proteins , vol.65 , Issue.3 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 42
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983; 79 (2): 926-935. doi: 10.1063/1.445869.
    • (1983) J Chem Phys , vol.79 , Issue.2 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3    Impey, R.W.4    Klein, M.L.5
  • 43
    • 33947425139 scopus 로고    scopus 로고
    • Hydration dynamics and time scales of coupled water-protein fluctuations
    • Li T, Hassanali AA, Kao Y-T, Zhong D, Singer SJ. Hydration dynamics and time scales of coupled water-protein fluctuations. J Am Chem Soc. 2007; 129 (11): 3376-3382. doi: 10.1021/ja0685957.
    • (2007) J Am Chem Soc , vol.129 , Issue.11 , pp. 3376-3382
    • Li, T.1    Hassanali, A.A.2    Kao, Y.-T.3    Zhong, D.4    Singer, S.J.5
  • 44
    • 84861229786 scopus 로고    scopus 로고
    • Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. Coli
    • Alijabbari N, Chen YK, Sizov I, Globus T, Gelmont B. Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli. J Mol Model. 2012; 18 (5): 2209-2218. doi: 10.1007/s00894-011-1238-6.
    • (2012) J Mol Model , vol.18 , Issue.5 , pp. 2209-2218
    • Alijabbari, N.1    Chen, Y.K.2    Sizov, I.3    Globus, T.4    Gelmont, B.5
  • 45
    • 84863419738 scopus 로고    scopus 로고
    • Temperature and hydration dependence of low-frequency spectra of poly-l-glutamic acid with different secondary structures studied by terahertz time-domain spectroscopy
    • Yamamoto N, Kambara O, Yamamoto K, Tamura A, Saito S, Tominaga K. Temperature and hydration dependence of low-frequency spectra of poly-l-glutamic acid with different secondary structures studied by terahertz time-domain spectroscopy. Soft Matter. 2012; 8 (6): 1997-2006. doi: 10.1039/C1SM06433A.
    • (2012) Soft Matter , vol.8 , Issue.6 , pp. 1997-2006
    • Yamamoto, N.1    Kambara, O.2    Yamamoto, K.3    Tamura, A.4    Saito, S.5    Tominaga, K.6
  • 46
  • 48
    • 77956209545 scopus 로고    scopus 로고
    • Combining THz spectroscopy and MD simulations to study protein-hydration coupling
    • Heyden M, Havenith M. Combining THz spectroscopy and MD simulations to study protein-hydration coupling. Methods. 2010; 52 (1): 74-83. doi: 10.1016/j.ymeth.2010.05.007.
    • (2010) Methods , vol.52 , Issue.1 , pp. 74-83
    • Heyden, M.1    Havenith, M.2
  • 49
    • 84945474814 scopus 로고    scopus 로고
    • Electrical properties and dielectric relaxation of DNA in solution
    • James B-J, Chriss A J, Bill R. Electrical properties and dielectric relaxation of DNA in solution. NIST Technical Note. 1998; 1509: 1-67.
    • (1998) NIST Technical Note , vol.1509 , pp. 1-67
    • James, B.-J.1    Chriss, A.J.2    Bill, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.