Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures
Abstract
Interactions with water are one of the key factors which determine protein stability and activity in aqueous solutions. However, the protein hydration is still insufficiently understood. N-methylacetamide (NMA) is regarded as a minimal part of the peptide backbone and the relative simplicity of its structure makes it a good model for studies on protein–water interactions. In this paper, the influence of NMA and N,N-dimethylacetamide (DMA) on surrounding water molecules in a range of temperature (25–75 ◦C) is studied by means of the FTIR spectroscopy. The results of the difference HDO spectra method are compared with the results of theoretical DFT calculations of NMA and DMA aqueous complexes. Both NMA and DMA can be regarded as “structure-makers”, yet their hydration spheres are different. These molecules exhibit a mixed and mutually dependent types of hydration: hydrophilic and hydrophobic. In the case of a NMA molecule that has one methyl group less than DMA, the type of hydrophobic hydration is more important. The DMA hydration sphere is less stable: the interactions between water molecules around the methyl groups are strained. Moreover, the hydration of NMA is much more temperature dependant than in the case of DMA. The source of the differences may be hidden in the N-H· · ·H2O interaction. The delicate nature of water interactions with the peptide block models may be cautiously translated into the much more complicated interactions of proteins with their hydration shells.
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- artykuł w czasopiśmie wyróżnionym w JCR
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JOURNAL OF MOLECULAR LIQUIDS
no. 278,
pages 706 - 715,
ISSN: 0167-7322 - Language:
- English
- Publication year:
- 2019
- Bibliographic description:
- Panuszko A., Nowak M., Bruździak P., Stasiulewicz M., Stangret J.: Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures// JOURNAL OF MOLECULAR LIQUIDS. -Vol. 278, (2019), s.706-715
- DOI:
- Digital Object Identifier (open in new tab) 10.1016/j.molliq.2019.01.086
- Bibliography: test
-
- L. Biedermannova, B. Schneider, Hydration of proteins and nucleic 462 acids: Advances in experiment and theory. A review, Biochim. Biophys. 463 Acta 1860 (2016) 1821-1835. open in new tab
- L. Aggarwal, P. Biswas, Hydration water distribution around intrinsi- 465 cally disordered proteins, J. Phys. Chem. B 122 (2018) 4206-4218. open in new tab
- J. N. Dahanayake, K. R. Mitchell-Koch, Entropy connects water struc- 467 ture and dynamics in protein hydration layers, Phys. Chem. Chem. open in new tab
- Phys. 20 (2018) 14765-14777. open in new tab
- J. T. King, K. J. Kubarych, Site-specific coupling of hydration water and 470 protein flexibility studied in solution with ultrafast 2D-IR spectroscopy, 471 open in new tab
- J. Am. Chem. Soc. 134 (2012) 18705-18712. open in new tab
- R. C. Remsing, E. Xi, A. J. Patel, Protein hydration thermodynamics: 473 The influence of flexibility and salt on hydrophobin II hydration, J. open in new tab
- Phys. Chem. B. 122 (2018) 3635-3646. open in new tab
- Amide II) and effect of solvation on the C=O stretch (Amide I) in- 520 tensity, J. Phys. Chem. 95 (1991) 2962-2967. open in new tab
- J. M. Dudik, C. R. Johnson, S. A. Asher, UV resonance Raman studies 522 of acetone, acetamide, and N-methylacetamide: Models for the peptide 523 bond, J. Phys. Chem. 89 (1985) 3805-3814. open in new tab
- X. G. Chen, R. Schweitzer-Stenner, N. G. Mirkin, S. A. Asher, N- 525 methylacetamide and its hydrogen-bonded water molecules are vibra- 526 tionally coupled, J. Am. Chem. Soc. 116 (1994) 11141-11142. open in new tab
- X. G. Chen, R. Schweitzer-Stenner, S. A. Asher, N. G. Mirkin, 528
- S. Krimm, Vibrational assignments of trans-N-methylacetamide and 529 some of its deuterated isotopomers from band decomposition of IR, visi- 530
- ble, and resonance Raman spectra, J. Phys. Chem. 99 (1995) 3074-3083.
- S. Song, S. A. Asher, S. Krimm, K. D. Shaw, Ultraviolet resonance 532 open in new tab
- Raman studies of trans and cis peptides: Photochemical consequences 533 of the twisted pi* excited state, J. Am. Chem. Soc. 113 (1991) 1155- 534 open in new tab
- V. Vasylyeva, S. K. Nayak, G. Terraneo, G. Cavallo, P. Metrangolo, 536 open in new tab
- G. Resnati, Orthogonal halogen and hydrogen bonds involving a peptide 537 bond model, CrystEngComm 16 (2014) 8102-8105.
- S. Woutersen, Y. Mu, G. Stock, P. Hamm, Hydrogen-bond lifetime 539 measured by time-resolved 2D-IR spectroscopy: N-methylacetamide in 540 methanol, Chemical Physics 266 (2001) 137-147. open in new tab
- M. F. DeCamp, L. DeFlores, J. M. McCracken, A. Tokmakoff, Amide I 542 vibrational dynamics of N-methylacetamide in polar solvents: The role 543 of electrostatic interactions, J. Phys. Chem. B 109 (2005) 11016-11026. open in new tab
- R. Schweitzer-Stenner, G. Sieler, Intermolecular coupling in liquid and 545 crystalline states of trans-N-methylacetamide investigated by polarized 546 open in new tab
- Raman and FT-IR spectroscopies, J. Phys. Chem. A 102 (1998) 118-
- R. Zhang, H. Li, Y. Lei, S. Han, All-atom Molecular Dynamic simula- 549 tions and relative NMR spectra study of weak c-h o contacts in amide- 550 water systems, J. Phys. Chem. B 109 (2005) 7482-7487. open in new tab
- V. K. Yadav, A. Chandra, First-principles simulation study of vibra- 552 tional spectral diffusion and hydrogen bond fluctuations in aqueous so- 553 lution of Nmethylacetamide, J. Phys. Chem. B 119 (2015) 9858-9867. open in new tab
- M. H. Farag, M. F. Ruiz-Lopez, A. Bastida, G. Monard, F. Ingrosso, 555 open in new tab
- Hydration effect on amide I infrared bands in water: An interpretation 556 based on an interaction energy decomposition scheme, J. Phys. Chem. 557 B 119 (2015) 9056-9067. open in new tab
- J. Heyda, J. C. Vincent, D. J. Tobias, J. Dzubiella, P. Jungwirth, Ion 559 specificity at the peptide bond: Molecular Dynamics simulations of N- 560 methylacetamide in aqueous salt solutions, J. Phys. Chem. B 114 (2010) 561 1213-1220. open in new tab
- W.-G. Han, S. Suhai, Density functional studies on N-methylacetamide- 563 water complexes, J. Phys. Chem. B 100 (1996) 3942-3949. open in new tab
- N. T. Hunt, K. Wynne, The effect of temperature and solvation on the 565 ultrafast dynamics of N-methylacetamide, Chem. Phys. Lett. 431 (2006) open in new tab
- N. G. Mirkin, S. Krimm, Ab initio vibrational analysis of isotopic deriva- 568 tives of aqueous hydrogen-bonded trans-N-methylacetamide, J. Mol. open in new tab
- Struct. 377 (1996) 219-234.
- J. Gao, M. Freindorf, Hybrid ab initio QM/MM simulation of N- 571 methylacetamide in aqueous solution, J. Phys. Chem. A 101 (1997) open in new tab
- A. Panuszko, E. Gojlo, J. Zielkiewicz, M. Smiechowski, J. Krakowiak, 574 open in new tab
- J. Stangret, Hydration of simple amides. FTIR spectra of HDO and 575 theoretical studies, J. Phys. Chem. B 112 (2008) 2483-2493.
- B. Mennucci, J. M. Martínez, How to model solvation of peptides? 577 Insights from a quantum-mechanical and molecular dynamics study of 578 open in new tab
- N-methylacetamide. 1. Geometries, infrared, and ultraviolet spectra in 579 water, Journal of Physical Chemistry B 109 (2005) 9818-9829.
- M. P. Gaigeot, R. Vuilleumier, M. Sprik, D. Borgis, Infrared spec- 581 troscopy of N-methylacetamide revisited by ab initio molecular dynam- 582 ics simulations, Journal of Chemical Theory and Computation 1 (2005) open in new tab
- M. Buck, M. Karplus, Hydrogen bond energetics: A simulation and 585 statistical analysis of N-methyl acetamide (NMA), water, and human 586 lysozyme, Journal of Physical Chemistry B 105 (2001) 11000-11015. 587 26 open in new tab
- Z.-Z. Yang, P. Qian, A study of N-methylacetamide in water clus- 588 ters: Based on atom-bond electronegativity equalization method fused 589 into molecular mechanics, The Journal of Chemical Physics 125 (2006) open in new tab
- W. L. Jorgensen, J. Gao, Cis-Trans energy difference for the peptide 592 bond in the gas phase and in aqueous solution, J. Am. Chem. Soc. 110 593 (1988) 4212-4216. open in new tab
- G. Nandini, D. N. Sathyanarayana, Ab initio studies on geometry and 595 vibrational spectra of N-methylformamide and N-methylacetamide, J. open in new tab
- Mol. Struct.(TEOCHEM) 579 (2002) 1-9. open in new tab
- S. Shin, A. Kurawaki, Y. Hamada, K. Shinya, K. Ohno, A. Tohara, 598 open in new tab
- M. Sato, Conformational behavior of N-methylformamide in the gas, 599 matrix, and solution states as revealed by IR and NMR spectroscopic 600 measurements and by theoretical calculations, J. Mol. Struct. 791 (2006) 601
- A. C. Fantoni, W. Caminati, Rotational spectrum and ab initio calcu- 603 lations of N-methylformamide, J. Chem. Soc., Faraday Trans. 92 (1996) open in new tab
- Y. K. Kang, H. S. Park, Internal rotation about the CN bond of amides, 606 open in new tab
- J. Mol. Struct.(TEOCHEM) 676 (2004) 171-176. open in new tab
- H. Torii, T. Tatsumi, M. Tasumi, Effects of hydration on the structure, 608 vibrational wavenumbers, vibrational force field and resonance raman 609 27 intensities ofN-methylacetamide, Journal of Raman Spectroscopy 29 610 (1998) 537-546. open in new tab
- M. P. Gaigeot, Theoretical spectroscopy of floppy peptides at room 612 temperature. A DFTMD perspective: Gas and aqueous phase, Physical 613 Chemistry Chemical Physics 12 (2010) 3336-3359. open in new tab
- F. Ingrosso, G. Monard, M. Hamdi Farag, A. Bastida, M. F. Ruiz-Lopez, 615 open in new tab
- Importance of Polarization and Charge Transfer Effects to Model the 616 open in new tab
- Infrared Spectra of Peptides in Solution, Journal of Chemical Theory 617 and Computation 7 (2011) 1840-1849. open in new tab
- K. Kwac, M. Cho, Molecular dynamics simulation study of <i>N</i> 619 -methylacetamide in water. I. Amide I mode frequency fluctuation, The 620 Journal of Chemical Physics 119 (2003) 2247-2255. open in new tab
- S. Ham, J.-H. Kim, H. Lee, M. Cho, Correlation between electronic and 622 molecular structure distortions and vibrational properties. II. Amide I 623 modes of NMAnD2O complexes, The Journal of Chemical Physics 118 624 (2003) 3491-3498. open in new tab
- M. Falk, T. A. Ford, Infrared spectrum and structure of liquid water, 626 open in new tab
- Can. J. Chem. 44 (1966) 1699-1707. open in new tab
- D. F. Hornig, On the spectrum and structure of water and ionic solu- 628 tions, J. Chem. Phys. 40 (1964) 3119. open in new tab
- J. Stangret, Solute-affected vibrational spectra of water in Ca(ClO 4 ) 2 630 aqueous solution, Spect. Lett. 21 (1988) 369-381. open in new tab
- J. Stangret, T. Gampe, Hydration sphere of tetrabutylammonium 632 cation. FTIR of HDO spectra, J. Phys. Chem. B 103 (1988) 3778-3783. open in new tab
- J. Stangret, T. Gampe, Ionic hydration behavior derived from infrared 634 spectra in HDO, J. Phys. Chem. A 106 (2002) 5393-5402. open in new tab
- M. Smiechowski, J. Stangret, Vibrational spectroscopy of semiheavy 636 water (HDO) as a probe of solute hydration, Pure Appl. Chem. 82 637 (2010) 1869-1887. open in new tab
- R. M. Badger, B. S. H. Bauer, Spectroscopic studies of the hydrogen 639 bond II the shift of the OH vibrational frequency in the formation of 640 the hydrogen bond, J. Chem. Phys. 5 (1937) 839-851. open in new tab
- S. Bratos, J.-C. Leicknam, S. Pommeret, Relation between the OH 642 stretching frequency and the OO distance in time-resolved infrared spec- 643 troscopy of hydrogen bonding, Chem. Phys. 359 (2009) 53-57. open in new tab
- M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, 645
- J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Pe- 646 tersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Iz- 647 maylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, 648
- K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, 649
- O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery Jr., J. E. Peralta, 650
- F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N.
- Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, 652 open in new tab
- J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, 653
- M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, 654 29 open in new tab
- R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, 655
- C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Za- 656 krzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D.
- Daniels,Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, 658
- E. R. Johnson, S. Keinan, P. Mori-Sanchez, J. Contreras-Garcia, A. J. open in new tab
- Cohen, W. Yang, Revealing noncovalent interactions, Journal of the 661
- American Chemical Society 132 (2010) 6498-6506. open in new tab
- T. Lu, F. Chen, Multiwfn: A multifunctional wavefunction analyzer, 663 Journal of Computational Chemistry 33 (2012) 580-592. open in new tab
- Taurine as a water structure breaker and protein stabilizer, Amino Acids 665 50 (2018) 125-140. open in new tab
- C. Lee, W. Yang, R. G. Parr, Development of the colle-salvetti 667 correlation-energy formula into a functional of the electron density, 668 open in new tab
- Physical Review B 37 (1988) 785-789. open in new tab
- A. D. Becke, Density-functional thermochemistry. III. the role of exact 670 exchange, The Journal of Chemical Physics 98 (1993) 5648-5652. open in new tab
- R. Ditchfield, W. J. Hehre, J. A. Pople, Self-consistent molecular-orbital 672 methods. IX. an extended gaussian-type basis for molecular-orbital stud- 673 ies of organic molecules, The Journal of Chemical Physics 54 (1971) open in new tab
- M. Cossi, N. Rega, G. Scalmani, V. Barone, Energies, structures, and 676 open in new tab
- model, Journal of Computational Chemistry 24 (2003) 669-681. open in new tab
- V. Barone, M. Cossi, Quantum calculation of molecular energies and 679 energy gradients in solution by a conductor solvent model, Journal of 680 Physical Chemistry A 102 (1998) 1995-2001. open in new tab
- S. Grimme, S. Ehrlich, L. Goerigk, Effect of the damping function in 682 dispersion corrected density functional theory, Journal of Computational 683 Chemistry 32 (2011) 1456-1465. open in new tab
- D. Eisenberg, W. Kauzmann, The Structure and Properties of Water., 685 open in new tab
- a Temperature ( o C). b Affected number, equal to the number of moles of water affected by one mole of solute. c Band position at maximum (cm −1 ). open in new tab
- d Band position at gravity center (cm −1 ). e Full width at half-height (cm −1 ). open in new tab
- f Integrated intensity (dm 3 · mol −1 · cm −1 ). g The most probable O· · · O dis- tance (Å). h Mean O· · · O distance (Å). open in new tab
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