Research progress of molecular structure and dynamics of biological water

Ye Shu-Ji; Li Chuan-Zhao; Zhang Jia-Hui; Tan Jun-Jun; Luo Yi

doi:10.7498/aps.68.20181273

Abstract

The specific water molecules that are confined within the solvation shell adjacent to the surface of biological macromolecules (including protein, enzyme, DNA, RNA, cell membrane, etc.) are called biological water molecules. Such water around the biomolecule surface plays a very important role in the structure, stability, dynamics, and function of biological macromolecules. A molecular-level understanding of the structure and dynamics of biological water, as well as the nature of its influence on biological structure and function is the key to revealing the mechanism of the biological functions. However, the researches in this field are still in the initial stage. Here in this paper, we review the relevant researches and recent progress of hydration water from three aspects. The first aspect is about the influence of hydration water on biological structure and function. It is evident that water actively participates in many biological processes such as protein folding, proton donation and migration, ligand binding and drug design, and allosteric effects. For example, water mediates the collapse of the chain and the search for the native topology through a funneled energy landscape. The second aspect is about the structure of water molecules around the biomolecules investigated by nuclear magnetic resonance (NMR), dielectric relaxation, neutron scattering, X-ray diffraction and ultrafast optical spectroscopy. The third aspect is about the dynamic behaviors of biological water, including the relaxation time scale, dynamic property, dynamic coupling between biomolecules and water molecules, and sub-diffusive motion of the water molecules along the protein surfaces. Different techniques measure different timescales for the motion of proteins and their hydration environment. While NMR and dielectric relaxation methods reveal the motion of biological water on a time scale from several tens of picoseconds to nanoseconds, ultrafast optical spectroscopy such as fluorescence and vibrational spectroscopy probes the hydrogen-bonding fluctuations of water on a time scale from the femtosecond to picosecond. It is therefore highly necessary to acquire a real and complete picture of the structure and dynamics of biological water by combining several different techniques. Finally, some unsolved scientific problems are also summarized in this review.

Keywords:

Authors and contacts

Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China

References

[1]	Kropman M F, Bakker H J 2001 Science 291 2118
[2]	Pal S K, Zewail A H 2004 Chem. Rev. 104 2099
[3]	Peon J, Pal S K, Zewail A H 2002 Proc. Natl. Acad. Sci. U.S.A. 99 10964
[4]	Bagchi B 2005 Chem. Rev. 105 3197
[5]	Watson J D, Crick F H C 1953 Nature 171 737
[6]	Ferrand M, Dianoux A J, Petry W, Zaccaï G 1993 Proc. Natl. Acad. Sci. U.S.A. 90 9668
[7]	Rupley J A, Careri G 1991 Adv. Protein Chem. 41 37
[8]	Kamal J K A, Zhao L, Zewail A H 2004 Proc. Natl. Acad. Sci. U.S.A. 101 13411
[9]	Pal S K, Peon J, Zewail A H 2002 Proc. Natl. Acad. Sci. U.S.A 99 15297
[10]	Chaplin M 2006 Nat. Rev. Mol. Cell Biol. 7 861
[11]	Bellissent-Funel M C, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia A E 2016 Chem. Rev. 116 7673
[12]	Nihonyanagi S, Yamaguchi S, Tahara T 2010 J. Am. Chem. Soc. 132 6867
[13]	Zhao W, Moilanen D E, Fenn E E, Fayer M D 2008 J. Am. Chem. Soc. 130 13927
[14]	Auer B, Kumar R, Schmidt J R, Skinner J L 2007 Proc. Natl. Acad. Sci. U.S.A. 104 14215
[15]	Laage D, Hynes J T 2006 Science 311 832
[16]	Fecko C J, Eaves J D, Loparo J J, Tokmakoff A, Geissler P L 2003 Science 301 1698
[17]	Mazur K, Heisler I A, Meech S R 2010 J. Phys. Chem. B 114 10684
[18]	Nibbering E T J, Elsaesser T 2004 Chem. Rev. 104 1887
[19]	Raschke T M 2006 Curr. Opin. Struct. Biol. 16 152
[20]	Bhattacharyya S M, Wang Z G, Zewail A H 2003 J. Phys. Chem. B 107 13218
[21]	Bhattacharyya K 2008 Chem. Commun. 0 2848
[22]	Levitt M, Sharon R 1988 Proc. Natl. Acad. Sci. U.S.A. 85 7557
[23]	Uda Y, Zepeda S, Kaneko F, Matsuura Y, Furukawa Y 2007 J. Phys. Chem. B 111 14355
[24]	Nandi N, Bagchi B 1997 J. Phys. Chem. B 101 10954
[25]	Pal S K, Peon J, Zewail A H 2002 Proc. Natl. Acad. Sci. U.S.A. 99 1763
[26]	Fenimore P W, Frauenfelder H, McMahon B H, Young R D 2004 Proc. Natl. Acad. Sci. U.S.A. 101 14408
[27]	Jana B, Pal S, Bagchi B 2012 J. Chem. Sci. 124 317
[28]	Zhong D P, Pal S K, Zewail A H 2011 Chem. Phys. Lett. 503 1
[29]	Biedermannová L, Schneider B 2016 Biochim. Biophys. Acta 1860 1821
[30]	Ball P 2008 Chem. Rev. 108 74
[31]	Laage D, Elsaesser T, Hynes J T 2017 Chem. Rev. 117 10694
[32]	Laage D, Elsaesser T, Hynes J T 2017 Struct. Dyn. 4 044018
[33]	Laage D, Elsaesser T, Hynes J T 2017 Struct. Dyn. 4 044018
[34]	Ball P 2017 Proc. Natl. Acad. Sci. U.S.A. 114 13327
[35]	Ball P 2008 ChemPhysChem 9 2677
[36]	Davis C M, Gruebele M, Sukenik S 2018 Curr. Opin. Struct. Biol. 48 23
[37]	Cheung M S, García A E, Onuchic J N 2002 Proc. Natl. Acad. Sci. U.S.A. 99 685
[38]	Vajda T, Perczel A 2014 J. Pept. Sci. 20 747
[39]	Dill K A, MacCallum J L 2012 Science 338 1042
[40]	Zwanzig R, Szabó A, Bagchi B 1992 Proc. Natl. Acad. Sci. U.S.A. 89 20
[41]	Levy Y, Onuchic J N 2006 Annu. Rev. Biophys. Biomol. Struct. 35 389
[42]	Chong S H, Ham S 2015 Acc. Chem. Res. 48 956
[43]	Thirumalai D, Reddy G, Straub J E 2012 Acc. Chem. Res. 45 83
[44]	Hu F H, Luo W B, Hong M 2010 Science 330 505
[45]	Hu F H, Schmidt-Rohr K, Hong M 2012 J. Am. Chem. Soc. 134 3703
[46]	Agmon N 1995 Chem. Phys. Lett. 244 456
[47]	Pinto L H, Dieckmann G R, Gandhi C S, Papworth C G, Braman J, Shaughnessy M A, Lear J D, Lamb R A, DeGrado W F 1997 Proc. Natl. Acad. Sci. U.S.A. 94 11301
[48]	Mould J A, Li H C, Dudlak C S, Lear J D, Pekosz A, Lamb R A, Pinto L H 2000 J. Biol. Chem. 275 8592
[49]	Swanson J M J, Maupin C M, Chen H, Petersen M K, Xu J C, Wu Y J, Voth G A 2007 J. Phys. Chem. B 111 4300
[50]	Hassanali A, Giberti F, Cuny J, Kühne T D, Parrinello M 2013 Proc. Natl. Acad. Sci. U.S.A. 110 13723
[51]	Kaila V R I, Wikström M, Hummer G 2014 Proc. Natl. Acad. Sci. U.S.A. 111 6988
[52]	Goyal P, Lu J X, Yang S, Gunner M R, Cui Q 2013 Proc. Natl. Acad. Sci. U.S.A. 110 18886
[53]	Lorch S, Capponi S, Pieront F, Bondar A N 2015 J. Phys. Chem. B 119 12172
[54]	Umena Y, Kawakami K, Shen J R, Kamiya N 2011 Nature 473 55
[55]	Hu X, Tan J J, Ye S J 2017 J. Phys. Chem. C 121 15181
[56]	Liu Y, Tan J J, Zhang J H, Li C Z, Luo Y, Ye S J 2018 Chem. Commun. 54 5903
[57]	Krimmer S G, Cramer J, Betz M, Fridh V, Karlsson R, Heine A, Klebe G 2016 J. Med. Chem. 59 10530
[58]	Grossman M, Born B, Heyden M, Tworowski D, Fields G B, Sagi I, Havenith M 2011 Nat. Struct. Mol. Biol. 18 1102
[59]	Ma C L, Polishchuk A L, Ohigashi Y, Stouffer A L, Schön A, Magavern E, Jing X H, Lear J D, Freire E, Lamb R A, DeGrado W F, Pinto L H 2009 Proc. Natl. Acad. Sci. U.S.A. 106 12283
[60]	Wu Y J, Voth G A 2005 Biophys. J. 89 2402
[61]	Gianti E, Carnevale V, DeGrado W F, Klein M L, Fiorin G 2015 J. Phys. Chem. B 119 1173
[62]	García-Sosa A T 2013 J. Chem. Inf. Model 53 1388
[63]	Wei D G, Wilson W D, Neidle S 2013 J. Am. Chem. Soc. 135 1369
[64]	Sadovsky E, Yifrach O 2007 Proc. Natl. Acad. Sci. U.S.A. 104 19813
[65]	Gnanasekaran R, Xu Y, Leitner D M 2010 J. Phys. Chem. B 114 16989
[66]	Oroguchi T, Nakasako M 2016 Sci. Rep. 6 26302
[67]	Buchli B, Waldauer S A, Walser R, Donten M L, Pfister R, Blöchliger N, Steiner S, Caflisch A, Zerbe O, Hamm P 2013 Proc. Natl. Acad. Sci. U.S.A. 110 11725
[68]	Sun T J, Lin F H, Campbell R L, Allingham J S, Davies P L 2014 Science 343 795
[69]	Lai W Z, Chen H, Matsui T, Omori K, Unno M, Ikeda-Saito M, Shaik S 2010 J. Am. Chem. Soc. 132 12960
[70]	Wang Y, Hirao H, Chen H, Onaka H, Nagano S, Shaik S 2008 J. Am. Chem. Soc. 130 7170
[71]	Weingarth M, van der Cruijsen E A W, Ostmeyer J, Lievestro S, Roux B, Baldus M 2014 J. Am. Chem. Soc. 136 2000
[72]	Hou G H, Cui Q 2013 J. Am. Chem. Soc. 135 10457
[73]	Pal R, Sekharan S, Batista V S 2013 J. Am. Chem. Soc. 135 9624
[74]	Ye S J, Markelz A 2010 J. Phys. Chem. B 114 15151
[75]	Stewart G W 1931 Phys. Rev. 37 9
[76]	Katzoff S 1934 J. Chem. Phys. 2 841
[77]	Eisenberg D, Kauzmann W 2005 The Structure and Properties of Water (New York: Oxford University Press) pp254-265
[78]	Wernet P, Nordlund D, Bergmann U, Cavalleri M, Odelius M, Ogasawara H, Naslund L Å, Hirsch T K, Ojamäe L, Glatzel P, Pettersson L G M, Nilsson A 2004 Science 304 995
[79]	Smith J D, Cappa C D, Wilson K R, Messer B M, Cohen R C, Saykally R J 2004 Science 306 851
[80]	Bukowski R, Szalewicz K, Groenenboom G C, van der Avoird A 2007 Science 315 1249
[81]	Tu Y S, Fang H P 2009 Phys. Rev. E 79 016707
[82]	Huang C, Wikfeldt K T, Tokushima T, Nordlund D, Harada Y, Bergmann U, Niebuhr M, Weiss T M, Horikawa Y, Leetmaa M, Ljungberg M P, Takahashi O, Lenz A, Ojamäe L, Lyubartsev A P, Shin S, Pettersson L G M, Nilsson A 2009 Proc. Natl. Acad. Sci. U.S.A. 106 15214
[83]	Smith J D, Cappa C D, Wilson K R, Cohen R C, Geissler P L, Saykally R J 2005 Proc. Natl. Acad. Sci. U.S.A. 102 14171
[84]	Nakasako M 2004 Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci. 359 1191
[85]	Burling F T, Weis W I, Flaherty K M, BrüngerA T 1996 Science 271 72
[86]	Teeter M M 1984 Proc. Natl. Acad. Sci. U.S.A. 81 6014
[87]	Sanschagrin P C, Kuhn L A 1998 Protein Sci. 7 2054
[88]	Kysilka J, Vondrášek J 2013 J. Mol. Recognit. 26 479
[89]	Schneider B, Berman H M 1995 Biophys. J. 69 2661
[90]	Schneider B, Patel K, Berman H M 1998 Biophys. J. 75 2422
[91]	Niimura N, Podjarny A 2011 Neutron Protein Crystallography: Hydrogen, Protons, and Hydration in Bio-Macromolecules (Vol. 25) (Oxford: Oxford University Press) pp124-189
[92]	Bellissent-Funel M C, Teixeira J, Bosio L 1987 J. Chem. Phys. 87 2231
[93]	Hong L, Smolin N, Lindner B, Sokolov A P, Smith J C 2011 Phys. Rev. Lett. 107 148102
[94]	Settles M, Doster W 1996 Faraday Discuss. 103 269
[95]	Angell C A 2004 Annu. Rev. Phys. Chem. 55 559
[96]	Du Q, Freysz E, Shen Y R 1994 Phys. Rev. Lett. 72 238
[97]	Shen Y R, Ostroverkhov V 2006 Chem. Rev. 106 1140
[98]	Du Q, Superfine R, Freysz E, Shen Y R 1993 Phys. Rev. Lett. 70 2313
[99]	Chen X K, Hua W, Huang Z S, Allen H C 2010 J. Am. Chem. Soc. 132 11336
[100]	Mondal J A, Nihonyanagi S, Yamaguchi S, Tahara T 2010 J. Am. Chem. Soc. 132 10656
[101]	Mondal J A, Nihonyanagi S, Yamaguchi S, Tahara T 2012 J. Am. Chem. Soc. 134 7842
[102]	Xu Y, Havenith M 2015 J. Chem. Phys. 143 170901
[103]	Papoian G A, Ulander J, Eastwood M P, Luthey-Schulten Z, Wolynes P G 2004 Proc. Natl. Acad. Sci. U.S.A. 101 3352
[104]	Heugen U, Schwaab G, Bründermann E, Heyden M, Yu X, Leitner D M, Havenith M 2006 Proc. Natl. Acad. Sci. U.S.A. 103 12301
[105]	Qvist J, Halle B 2008 J. Am. Chem. Soc. 130 10345
[106]	Born B, Weingärtner H, Bründermann E, Havenith M 2009 J. Am. Chem. Soc. 131 3752
[107]	Oncley J L 1938 J. Am. Chem. Soc. 60 1115
[108]	Oncley J L 1943 in: Cohn E J, Edsall J T ed. Proteins, Amino Acids and Peptides as Ions and Dipolar Ions (Chapter 22) (New York: Reinhold) p557
[109]	Buchanan T J, Haggis G H, Hasted J B, Robinson B G 1952 Proc. R. Soc. London A 213 379
[110]	Haggis G H, Buchanan T J, Hasted J B 1951 Nature 167 607
[111]	Grant E H 1965 Ann. NY Acad. Sci. 125 418
[112]	Grant E H, Sheppard R J, South G P 1978 Dielectric Behavior of Biological Molecules in Solutions (Oxford: Clarendon) pp144-160
[113]	Schwan H P 1965 Ann. NY Acad. Sci. 125 344
[114]	Takashima S 1967 Adv. Chem. Ser. 63 232
[115]	Harvey S C, Hoekstra P 1972 J. Phys. Chem. 76 2987
[116]	Pethig R 1995 in: Gregory R B ed. Protein Solvent Interactions (Chapter 4) (New York: Marcel Dekker Inc.) pp265–285
[117]	Murarka R K, Head-Gordon T 2008 J. Phys. Chem. B 112 179
[118]	Otting G, Liepinsh E, Wuthrich K 1991 Science 254 974
[119]	Denisov V P, Halle B 1996 Faraday Discuss. 103 227
[120]	Modig K, Liepinsh E, Otting G, Halle B 2004 J. Am. Chem. Soc. 126 102
[121]	Grebenkov D S, Goddard Y A, Diakova G, Korb J P, Bryant R G 2009 J. Phys. Chem. B 113 13347
[122]	Bagchi B 2016 Proc. Natl. Acad. Sci. U.S.A. 113 8355
[123]	Qiu W H, Kao Y T, Zhang L Y, Yang Y, Wang L J, Stites W E, Zhong D P, Zewail A H 2006 Proc. Natl. Acad. Sci. U.S.A. 103 13979
[124]	Zhang L Y, Wang L J, Kao Y T, Qiu W H, Yang Y, Okobiah O, Zhong D P 2007 Proc. Natl. Acad. Sci. U.S.A. 104 18461
[125]	Zhang L Y, Yang Y, Kao Y T, Wang L J, Zhong D P 2009 J. Am. Chem. Soc. 131 10677
[126]	Frauenfelder H, Chen G, Berendzen J, Fenimore P W, Jansson H, McMahon B H, Stroe I R, Swenson J, Young R D 2009 Proc. Natl. Acad. Sci. U.S.A. 106 5129
[127]	Qin Y Z, Wang L J, Zhong D P 2016 Proc. Natl. Acad. Sci. U.S.A. 113 8424
[128]	Qin Y Z, Yang Y, Wang L J, Zhong D P 2017 Chem. Phys. Lett. 683 658
[129]	Qin Y Z, Jia M H, Yang J, Wang D H, Wang L J, Xu J H, Zhong D P 2016 J. Phys. Chem. Lett. 7 4171
[130]	Yang J, Wang Y F, Wang L J, Zhong D P 2017 J. Am. Chem. Soc. 139 4399
[131]	Bakker H J, Skinner J L 2010 Chem. Rev. 110 1498
[132]	Wright J C 2011 Annu. Rev. Phys. Chem. 62 209
[133]	Yagasaki T, Saito S 2009 Acc. Chem. Res. 42 1250
[134]	Roberts S T, Ramasesha K, Tokmakoff A 2009 Acc. Chem. Res. 42 1239
[135]	Bakulin A A, Liang C W, Jansen T L C, Wiersma D A, Bakker H J, Pshenichnikov M S 2009 Acc. Chem. Res. 42 1229
[136]	Ghosh R, Samanta T, Banaerjee S, Biswas R, Bagchi B 2015 Faraday Discuss. 177 313
[137]	King J T, Kubarych K J 2012 J. Am. Chem. Soc. 134 18705
[138]	McGuire J A, Shen Y R 2006 Science 313 1945
[139]	Zhang Z, Piatkowski L, Bakker H J, Bonn M 2011 Nature Chem. 3 888
[140]	Kel O, Tamimi A, Thielges M C, Fayer M D 2013 J. Am. Chem. Soc. 135 11063
[141]	Kundu A, Błasiak B, Lim J H, Kwak K, Cho M 2016 J. Phys. Chem. Lett. 7 741
[142]	Donovan M A, Yimer Y Y, Pfaendtner J, Backus E H G, Bonn M, Weidner T 2016 J. Am. Chem. Soc. 138 5226
[143]	Pandey R, Usui K, Livingstone R A, Fischer S A, Pfaendtner J, Backus E H G, Nagata Y, Fröhlich- Nowoisky J, Schmüser L, Mauri S, Scheel J F, Knopf D A, Pöschl U, Bonn M, Weidner T 2016 Sci. Adv. 2 e1501630
[144]	Zhang Z, Piatkowski L, Bakker H J, Bonn M 2011 J. Chem. Phys. 135 021101
[145]	Ohto T, Backus E H G, Hsieh C S, Sulpizi M, Bonn M, Nagata Y 2015 J. Phys. Chem. Lett. 6 4499
[146]	Livingstone R A, Nagata Y, Bonn M, Backus E H G 2015 J. Am. Chem. Soc. 137 14912
[147]	Tan J J, Zhang B X, Luo Y, Ye S J 2017 Angew. Chem. Int. Ed. 56 12977
[148]	Tan J J, Luo Y, Ye S J 2017 Chin. J. Chem. Phys. 30 671
[149]	Tan P, Liang Y H, Xu Q, Mamontov E, Li J L, Xing X J, Hong L 2018 Phys. Rev. Lett. 120 248101
[150]	Metzler R 2018 Physics 11 59
[151]	Perticaroli S, Ehlers G, Stanley C B, Mamontov E, O’Neill H, Zhang Q, Cheng X L, Myles D A A, Katsaras J, Nickels J D 2017 J. Am. Chem. Soc. 139 1098
[152]	von Hansen Y, Gekle S, Netz R R 2013 Phys. Rev. Lett. 111 118103
[153]	Bizzarri A R, Cannistraro S 2002 J. Phys. Chem. B 106 6617
[154]	Bizzarri A R, Rocchi C, Cannistraro S 1996 Chem. Phys. Lett. 263 559
[155]	Pizzitutti F, Marchi M, Sterpone F, Rossky P J 2007 J. Phys. Chem. B 111 7584

Cited By

[1]	Kropman M F, Bakker H J 2001 Science 291 2118
[2]	Pal S K, Zewail A H 2004 Chem. Rev. 104 2099
[3]	Peon J, Pal S K, Zewail A H 2002 Proc. Natl. Acad. Sci. U.S.A. 99 10964
[4]	Bagchi B 2005 Chem. Rev. 105 3197
[5]	Watson J D, Crick F H C 1953 Nature 171 737
[6]	Ferrand M, Dianoux A J, Petry W, Zaccaï G 1993 Proc. Natl. Acad. Sci. U.S.A. 90 9668
[7]	Rupley J A, Careri G 1991 Adv. Protein Chem. 41 37
[8]	Kamal J K A, Zhao L, Zewail A H 2004 Proc. Natl. Acad. Sci. U.S.A. 101 13411
[9]	Pal S K, Peon J, Zewail A H 2002 Proc. Natl. Acad. Sci. U.S.A 99 15297
[10]	Chaplin M 2006 Nat. Rev. Mol. Cell Biol. 7 861
[11]	Bellissent-Funel M C, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia A E 2016 Chem. Rev. 116 7673
[12]	Nihonyanagi S, Yamaguchi S, Tahara T 2010 J. Am. Chem. Soc. 132 6867
[13]	Zhao W, Moilanen D E, Fenn E E, Fayer M D 2008 J. Am. Chem. Soc. 130 13927
[14]	Auer B, Kumar R, Schmidt J R, Skinner J L 2007 Proc. Natl. Acad. Sci. U.S.A. 104 14215
[15]	Laage D, Hynes J T 2006 Science 311 832
[16]	Fecko C J, Eaves J D, Loparo J J, Tokmakoff A, Geissler P L 2003 Science 301 1698
[17]	Mazur K, Heisler I A, Meech S R 2010 J. Phys. Chem. B 114 10684
[18]	Nibbering E T J, Elsaesser T 2004 Chem. Rev. 104 1887
[19]	Raschke T M 2006 Curr. Opin. Struct. Biol. 16 152
[20]	Bhattacharyya S M, Wang Z G, Zewail A H 2003 J. Phys. Chem. B 107 13218
[21]	Bhattacharyya K 2008 Chem. Commun. 0 2848
[22]	Levitt M, Sharon R 1988 Proc. Natl. Acad. Sci. U.S.A. 85 7557
[23]	Uda Y, Zepeda S, Kaneko F, Matsuura Y, Furukawa Y 2007 J. Phys. Chem. B 111 14355
[24]	Nandi N, Bagchi B 1997 J. Phys. Chem. B 101 10954
[25]	Pal S K, Peon J, Zewail A H 2002 Proc. Natl. Acad. Sci. U.S.A. 99 1763
[26]	Fenimore P W, Frauenfelder H, McMahon B H, Young R D 2004 Proc. Natl. Acad. Sci. U.S.A. 101 14408
[27]	Jana B, Pal S, Bagchi B 2012 J. Chem. Sci. 124 317
[28]	Zhong D P, Pal S K, Zewail A H 2011 Chem. Phys. Lett. 503 1
[29]	Biedermannová L, Schneider B 2016 Biochim. Biophys. Acta 1860 1821
[30]	Ball P 2008 Chem. Rev. 108 74
[31]	Laage D, Elsaesser T, Hynes J T 2017 Chem. Rev. 117 10694
[32]	Laage D, Elsaesser T, Hynes J T 2017 Struct. Dyn. 4 044018
[33]	Laage D, Elsaesser T, Hynes J T 2017 Struct. Dyn. 4 044018
[34]	Ball P 2017 Proc. Natl. Acad. Sci. U.S.A. 114 13327
[35]	Ball P 2008 ChemPhysChem 9 2677
[36]	Davis C M, Gruebele M, Sukenik S 2018 Curr. Opin. Struct. Biol. 48 23
[37]	Cheung M S, García A E, Onuchic J N 2002 Proc. Natl. Acad. Sci. U.S.A. 99 685
[38]	Vajda T, Perczel A 2014 J. Pept. Sci. 20 747
[39]	Dill K A, MacCallum J L 2012 Science 338 1042
[40]	Zwanzig R, Szabó A, Bagchi B 1992 Proc. Natl. Acad. Sci. U.S.A. 89 20
[41]	Levy Y, Onuchic J N 2006 Annu. Rev. Biophys. Biomol. Struct. 35 389
[42]	Chong S H, Ham S 2015 Acc. Chem. Res. 48 956
[43]	Thirumalai D, Reddy G, Straub J E 2012 Acc. Chem. Res. 45 83
[44]	Hu F H, Luo W B, Hong M 2010 Science 330 505
[45]	Hu F H, Schmidt-Rohr K, Hong M 2012 J. Am. Chem. Soc. 134 3703
[46]	Agmon N 1995 Chem. Phys. Lett. 244 456
[47]	Pinto L H, Dieckmann G R, Gandhi C S, Papworth C G, Braman J, Shaughnessy M A, Lear J D, Lamb R A, DeGrado W F 1997 Proc. Natl. Acad. Sci. U.S.A. 94 11301
[48]	Mould J A, Li H C, Dudlak C S, Lear J D, Pekosz A, Lamb R A, Pinto L H 2000 J. Biol. Chem. 275 8592
[49]	Swanson J M J, Maupin C M, Chen H, Petersen M K, Xu J C, Wu Y J, Voth G A 2007 J. Phys. Chem. B 111 4300
[50]	Hassanali A, Giberti F, Cuny J, Kühne T D, Parrinello M 2013 Proc. Natl. Acad. Sci. U.S.A. 110 13723
[51]	Kaila V R I, Wikström M, Hummer G 2014 Proc. Natl. Acad. Sci. U.S.A. 111 6988
[52]	Goyal P, Lu J X, Yang S, Gunner M R, Cui Q 2013 Proc. Natl. Acad. Sci. U.S.A. 110 18886
[53]	Lorch S, Capponi S, Pieront F, Bondar A N 2015 J. Phys. Chem. B 119 12172
[54]	Umena Y, Kawakami K, Shen J R, Kamiya N 2011 Nature 473 55
[55]	Hu X, Tan J J, Ye S J 2017 J. Phys. Chem. C 121 15181
[56]	Liu Y, Tan J J, Zhang J H, Li C Z, Luo Y, Ye S J 2018 Chem. Commun. 54 5903
[57]	Krimmer S G, Cramer J, Betz M, Fridh V, Karlsson R, Heine A, Klebe G 2016 J. Med. Chem. 59 10530
[58]	Grossman M, Born B, Heyden M, Tworowski D, Fields G B, Sagi I, Havenith M 2011 Nat. Struct. Mol. Biol. 18 1102
[59]	Ma C L, Polishchuk A L, Ohigashi Y, Stouffer A L, Schön A, Magavern E, Jing X H, Lear J D, Freire E, Lamb R A, DeGrado W F, Pinto L H 2009 Proc. Natl. Acad. Sci. U.S.A. 106 12283
[60]	Wu Y J, Voth G A 2005 Biophys. J. 89 2402
[61]	Gianti E, Carnevale V, DeGrado W F, Klein M L, Fiorin G 2015 J. Phys. Chem. B 119 1173
[62]	García-Sosa A T 2013 J. Chem. Inf. Model 53 1388
[63]	Wei D G, Wilson W D, Neidle S 2013 J. Am. Chem. Soc. 135 1369
[64]	Sadovsky E, Yifrach O 2007 Proc. Natl. Acad. Sci. U.S.A. 104 19813
[65]	Gnanasekaran R, Xu Y, Leitner D M 2010 J. Phys. Chem. B 114 16989
[66]	Oroguchi T, Nakasako M 2016 Sci. Rep. 6 26302
[67]	Buchli B, Waldauer S A, Walser R, Donten M L, Pfister R, Blöchliger N, Steiner S, Caflisch A, Zerbe O, Hamm P 2013 Proc. Natl. Acad. Sci. U.S.A. 110 11725
[68]	Sun T J, Lin F H, Campbell R L, Allingham J S, Davies P L 2014 Science 343 795
[69]	Lai W Z, Chen H, Matsui T, Omori K, Unno M, Ikeda-Saito M, Shaik S 2010 J. Am. Chem. Soc. 132 12960
[70]	Wang Y, Hirao H, Chen H, Onaka H, Nagano S, Shaik S 2008 J. Am. Chem. Soc. 130 7170
[71]	Weingarth M, van der Cruijsen E A W, Ostmeyer J, Lievestro S, Roux B, Baldus M 2014 J. Am. Chem. Soc. 136 2000
[72]	Hou G H, Cui Q 2013 J. Am. Chem. Soc. 135 10457
[73]	Pal R, Sekharan S, Batista V S 2013 J. Am. Chem. Soc. 135 9624
[74]	Ye S J, Markelz A 2010 J. Phys. Chem. B 114 15151
[75]	Stewart G W 1931 Phys. Rev. 37 9
[76]	Katzoff S 1934 J. Chem. Phys. 2 841
[77]	Eisenberg D, Kauzmann W 2005 The Structure and Properties of Water (New York: Oxford University Press) pp254-265
[78]	Wernet P, Nordlund D, Bergmann U, Cavalleri M, Odelius M, Ogasawara H, Naslund L Å, Hirsch T K, Ojamäe L, Glatzel P, Pettersson L G M, Nilsson A 2004 Science 304 995
[79]	Smith J D, Cappa C D, Wilson K R, Messer B M, Cohen R C, Saykally R J 2004 Science 306 851
[80]	Bukowski R, Szalewicz K, Groenenboom G C, van der Avoird A 2007 Science 315 1249
[81]	Tu Y S, Fang H P 2009 Phys. Rev. E 79 016707
[82]	Huang C, Wikfeldt K T, Tokushima T, Nordlund D, Harada Y, Bergmann U, Niebuhr M, Weiss T M, Horikawa Y, Leetmaa M, Ljungberg M P, Takahashi O, Lenz A, Ojamäe L, Lyubartsev A P, Shin S, Pettersson L G M, Nilsson A 2009 Proc. Natl. Acad. Sci. U.S.A. 106 15214
[83]	Smith J D, Cappa C D, Wilson K R, Cohen R C, Geissler P L, Saykally R J 2005 Proc. Natl. Acad. Sci. U.S.A. 102 14171
[84]	Nakasako M 2004 Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci. 359 1191
[85]	Burling F T, Weis W I, Flaherty K M, BrüngerA T 1996 Science 271 72
[86]	Teeter M M 1984 Proc. Natl. Acad. Sci. U.S.A. 81 6014
[87]	Sanschagrin P C, Kuhn L A 1998 Protein Sci. 7 2054
[88]	Kysilka J, Vondrášek J 2013 J. Mol. Recognit. 26 479
[89]	Schneider B, Berman H M 1995 Biophys. J. 69 2661
[90]	Schneider B, Patel K, Berman H M 1998 Biophys. J. 75 2422
[91]	Niimura N, Podjarny A 2011 Neutron Protein Crystallography: Hydrogen, Protons, and Hydration in Bio-Macromolecules (Vol. 25) (Oxford: Oxford University Press) pp124-189
[92]	Bellissent-Funel M C, Teixeira J, Bosio L 1987 J. Chem. Phys. 87 2231
[93]	Hong L, Smolin N, Lindner B, Sokolov A P, Smith J C 2011 Phys. Rev. Lett. 107 148102
[94]	Settles M, Doster W 1996 Faraday Discuss. 103 269
[95]	Angell C A 2004 Annu. Rev. Phys. Chem. 55 559
[96]	Du Q, Freysz E, Shen Y R 1994 Phys. Rev. Lett. 72 238
[97]	Shen Y R, Ostroverkhov V 2006 Chem. Rev. 106 1140
[98]	Du Q, Superfine R, Freysz E, Shen Y R 1993 Phys. Rev. Lett. 70 2313
[99]	Chen X K, Hua W, Huang Z S, Allen H C 2010 J. Am. Chem. Soc. 132 11336
[100]	Mondal J A, Nihonyanagi S, Yamaguchi S, Tahara T 2010 J. Am. Chem. Soc. 132 10656
[101]	Mondal J A, Nihonyanagi S, Yamaguchi S, Tahara T 2012 J. Am. Chem. Soc. 134 7842
[102]	Xu Y, Havenith M 2015 J. Chem. Phys. 143 170901
[103]	Papoian G A, Ulander J, Eastwood M P, Luthey-Schulten Z, Wolynes P G 2004 Proc. Natl. Acad. Sci. U.S.A. 101 3352
[104]	Heugen U, Schwaab G, Bründermann E, Heyden M, Yu X, Leitner D M, Havenith M 2006 Proc. Natl. Acad. Sci. U.S.A. 103 12301
[105]	Qvist J, Halle B 2008 J. Am. Chem. Soc. 130 10345
[106]	Born B, Weingärtner H, Bründermann E, Havenith M 2009 J. Am. Chem. Soc. 131 3752
[107]	Oncley J L 1938 J. Am. Chem. Soc. 60 1115
[108]	Oncley J L 1943 in: Cohn E J, Edsall J T ed. Proteins, Amino Acids and Peptides as Ions and Dipolar Ions (Chapter 22) (New York: Reinhold) p557
[109]	Buchanan T J, Haggis G H, Hasted J B, Robinson B G 1952 Proc. R. Soc. London A 213 379
[110]	Haggis G H, Buchanan T J, Hasted J B 1951 Nature 167 607
[111]	Grant E H 1965 Ann. NY Acad. Sci. 125 418
[112]	Grant E H, Sheppard R J, South G P 1978 Dielectric Behavior of Biological Molecules in Solutions (Oxford: Clarendon) pp144-160
[113]	Schwan H P 1965 Ann. NY Acad. Sci. 125 344
[114]	Takashima S 1967 Adv. Chem. Ser. 63 232
[115]	Harvey S C, Hoekstra P 1972 J. Phys. Chem. 76 2987
[116]	Pethig R 1995 in: Gregory R B ed. Protein Solvent Interactions (Chapter 4) (New York: Marcel Dekker Inc.) pp265–285
[117]	Murarka R K, Head-Gordon T 2008 J. Phys. Chem. B 112 179
[118]	Otting G, Liepinsh E, Wuthrich K 1991 Science 254 974
[119]	Denisov V P, Halle B 1996 Faraday Discuss. 103 227
[120]	Modig K, Liepinsh E, Otting G, Halle B 2004 J. Am. Chem. Soc. 126 102
[121]	Grebenkov D S, Goddard Y A, Diakova G, Korb J P, Bryant R G 2009 J. Phys. Chem. B 113 13347
[122]	Bagchi B 2016 Proc. Natl. Acad. Sci. U.S.A. 113 8355
[123]	Qiu W H, Kao Y T, Zhang L Y, Yang Y, Wang L J, Stites W E, Zhong D P, Zewail A H 2006 Proc. Natl. Acad. Sci. U.S.A. 103 13979
[124]	Zhang L Y, Wang L J, Kao Y T, Qiu W H, Yang Y, Okobiah O, Zhong D P 2007 Proc. Natl. Acad. Sci. U.S.A. 104 18461
[125]	Zhang L Y, Yang Y, Kao Y T, Wang L J, Zhong D P 2009 J. Am. Chem. Soc. 131 10677
[126]	Frauenfelder H, Chen G, Berendzen J, Fenimore P W, Jansson H, McMahon B H, Stroe I R, Swenson J, Young R D 2009 Proc. Natl. Acad. Sci. U.S.A. 106 5129
[127]	Qin Y Z, Wang L J, Zhong D P 2016 Proc. Natl. Acad. Sci. U.S.A. 113 8424
[128]	Qin Y Z, Yang Y, Wang L J, Zhong D P 2017 Chem. Phys. Lett. 683 658
[129]	Qin Y Z, Jia M H, Yang J, Wang D H, Wang L J, Xu J H, Zhong D P 2016 J. Phys. Chem. Lett. 7 4171
[130]	Yang J, Wang Y F, Wang L J, Zhong D P 2017 J. Am. Chem. Soc. 139 4399
[131]	Bakker H J, Skinner J L 2010 Chem. Rev. 110 1498
[132]	Wright J C 2011 Annu. Rev. Phys. Chem. 62 209
[133]	Yagasaki T, Saito S 2009 Acc. Chem. Res. 42 1250
[134]	Roberts S T, Ramasesha K, Tokmakoff A 2009 Acc. Chem. Res. 42 1239
[135]	Bakulin A A, Liang C W, Jansen T L C, Wiersma D A, Bakker H J, Pshenichnikov M S 2009 Acc. Chem. Res. 42 1229
[136]	Ghosh R, Samanta T, Banaerjee S, Biswas R, Bagchi B 2015 Faraday Discuss. 177 313
[137]	King J T, Kubarych K J 2012 J. Am. Chem. Soc. 134 18705
[138]	McGuire J A, Shen Y R 2006 Science 313 1945
[139]	Zhang Z, Piatkowski L, Bakker H J, Bonn M 2011 Nature Chem. 3 888
[140]	Kel O, Tamimi A, Thielges M C, Fayer M D 2013 J. Am. Chem. Soc. 135 11063
[141]	Kundu A, Błasiak B, Lim J H, Kwak K, Cho M 2016 J. Phys. Chem. Lett. 7 741
[142]	Donovan M A, Yimer Y Y, Pfaendtner J, Backus E H G, Bonn M, Weidner T 2016 J. Am. Chem. Soc. 138 5226
[143]	Pandey R, Usui K, Livingstone R A, Fischer S A, Pfaendtner J, Backus E H G, Nagata Y, Fröhlich- Nowoisky J, Schmüser L, Mauri S, Scheel J F, Knopf D A, Pöschl U, Bonn M, Weidner T 2016 Sci. Adv. 2 e1501630
[144]	Zhang Z, Piatkowski L, Bakker H J, Bonn M 2011 J. Chem. Phys. 135 021101
[145]	Ohto T, Backus E H G, Hsieh C S, Sulpizi M, Bonn M, Nagata Y 2015 J. Phys. Chem. Lett. 6 4499
[146]	Livingstone R A, Nagata Y, Bonn M, Backus E H G 2015 J. Am. Chem. Soc. 137 14912
[147]	Tan J J, Zhang B X, Luo Y, Ye S J 2017 Angew. Chem. Int. Ed. 56 12977
[148]	Tan J J, Luo Y, Ye S J 2017 Chin. J. Chem. Phys. 30 671
[149]	Tan P, Liang Y H, Xu Q, Mamontov E, Li J L, Xing X J, Hong L 2018 Phys. Rev. Lett. 120 248101
[150]	Metzler R 2018 Physics 11 59
[151]	Perticaroli S, Ehlers G, Stanley C B, Mamontov E, O’Neill H, Zhang Q, Cheng X L, Myles D A A, Katsaras J, Nickels J D 2017 J. Am. Chem. Soc. 139 1098
[152]	von Hansen Y, Gekle S, Netz R R 2013 Phys. Rev. Lett. 111 118103
[153]	Bizzarri A R, Cannistraro S 2002 J. Phys. Chem. B 106 6617
[154]	Bizzarri A R, Rocchi C, Cannistraro S 1996 Chem. Phys. Lett. 263 559
[155]	Pizzitutti F, Marchi M, Sterpone F, Rossky P J 2007 J. Phys. Chem. B 111 7584

[1]	Fang Zhen, Yu You, Zhao Qiu-Ye, Zhang Yu-Dong, Wang Zhi-Qiang, Zhang Zu-Xing. Spectral pulsation dynamics of soliton molecules in ultrafast fiber lasers based on pump intensity modulation. Acta Physica Sinica, 2024, 73(1): 014202. doi: 10.7498/aps.73.20231030
[2]	Jia Yun-Zhe, Meng Sheng. Ultrafast dynamics of water system under photoexcitation. Acta Physica Sinica, 2024, 73(8): 084204. doi: 10.7498/aps.73.20240047
[3]	Zhang Yu-Hang, Xue Zhen-Yong, Sun Hao, Zhang Zhu-Wei, Chen Hu. Single molecule magnetic tweezers for unfolding dynamics of Acyl-CoA binding protein. Acta Physica Sinica, 2023, 72(15): 158702. doi: 10.7498/aps.72.20230533
[4]	Tao Chen-Yu, Lei Jian-Ting, Yu Xuan, Luo Yan, Ma Xin-Wen, Zhang Shao-Feng. Development of attosecond pulses and their application to ultrafast dynamics of atoms and molecules. Acta Physica Sinica, 2023, 72(5): 053202. doi: 10.7498/aps.72.20222436
[5]	Xiang Mei, Ling Feng-Zi, Deng Xu-Lan, Wei Jie, Bumaliya Abulimiti, Zhang Bing. Ultrafast dynamics of electron excited states of phenylacetylene. Acta Physica Sinica, 2021, 70(5): 053302. doi: 10.7498/aps.70.20201473
[6]	Qin Chao-Chao, Cui Ming-Huan, Song Di-Di, He Wei. Ultrafast multiexciton Auger recombination of CdSeS. Acta Physica Sinica, 2019, 68(10): 107801. doi: 10.7498/aps.68.20190291
[7]	Wang Qiang, Cao Ze-Xian. Definition and quantification of hydration water in aqueous solutions. Acta Physica Sinica, 2019, 68(1): 015101. doi: 10.7498/aps.68.20181742
[8]	Lu Yue, Ma Jian-Bing, Teng Cui-Juan, Lu Ying, Li Ming, Xu Chun-Hua. Binding process between E.coli SSB and ssDNA by single-molecule dynamics. Acta Physica Sinica, 2018, 67(8): 088201. doi: 10.7498/aps.67.20180109
[9]	Chen Cong, Liang Pan, Hu Rong-Rong, Jia Tian-Qing, Sun Zhen-Rong, Feng Dong-Hai. Pump-orientation-probe technique and its applications. Acta Physica Sinica, 2018, 67(9): 097201. doi: 10.7498/aps.67.20180244
[10]	Yin Ling-Kang, Xu Shun, Seongmin Jeong, Yongseok Jho, Wang Jian-Jun, Zhou Xin. Vapor-liquid coexisting morphology of all-atom water model through generalized isothermal isobaric ensemble molecular dynamics simulation. Acta Physica Sinica, 2017, 66(13): 136102. doi: 10.7498/aps.66.136102
[11]	Luo Jin-Long, Ling Feng-Zi, Li Shuai, Wang Yan-Mei, Zhang Bing. Ultrafast photodissociation dynamics of butanone in 3s Rydberg state. Acta Physica Sinica, 2017, 66(2): 023301. doi: 10.7498/aps.66.023301
[12]	Liu Can-Dong, Jia Zheng-Mao, Zheng Ying-Hui, Ge Xiao-Chun, Zeng Zhi-Nan, Li Ru-Xin. Research progress of the control and measurement of the atomic and molecular ultrafast electron dynamics using two-color field. Acta Physica Sinica, 2016, 65(22): 223206. doi: 10.7498/aps.65.223206
[13]	Xia Dong, Wang Xin-Qiang. Structures and melting behaviors of ultrathin platinum nanowires. Acta Physica Sinica, 2012, 61(13): 130510. doi: 10.7498/aps.61.130510
[14]	Liu Hua-Min, Fan Yong-Sheng, Tian Shi-Hai, Zhou Wei, Chen Xu. Molecular dynamics simulation for the effect of hydrogen on the water of pressurized water reactors. Acta Physica Sinica, 2012, 61(6): 062801. doi: 10.7498/aps.61.062801
[15]	Li Xia, Feng Dong-Hai, He Hong-Yan, Jia Tian-Qing, Shan Lu-Fan, Sun Zhen-Rong, Xu Zhi-Zhan. Ultrafast carrier dynamics in CdTe/CdS Core/Shell quantum dots. Acta Physica Sinica, 2012, 61(19): 197801. doi: 10.7498/aps.61.197801
[16]	Shi Shun-Ping, Li Yong, Fan Yong-Sheng, Chen Xu, Zhou Wei. Molecular dynamics simulation for the impact of hydrazineon the water of pressurized water reactors. Acta Physica Sinica, 2011, 60(3): 032802. doi: 10.7498/aps.60.032802
[17]	Li Chun, Yang Fan, Georgios Lefkidis, Wolfgang Hübner. Laser-induced ultrafast spin dynamics research on magnetic nanostructures. Acta Physica Sinica, 2011, 60(1): 017802. doi: 10.7498/aps.60.017802
[18]	Gao Rui-Xin, Xu Zhen, Chen Da-Xin, Xu Chu-Dong, Chen Zhi-Feng, Liu Xiao-Dong, Zhou Shi-Ming, Lai Tian-Shu. RE-TM antiferromagnetic coupling and laser induced ultrafast magnetization reversal dynamics in GdFeCo magneto-optical films. Acta Physica Sinica, 2009, 58(1): 580-584. doi: 10.7498/aps.58.580
[19]	Yan Ke-Feng, Li Xiao-Sen, Chen Zhao-Yang, Li Gang, Li Zhi-Bao. Molecular dynamics simulation of methane hydrate dissociation by thermal stimulation in conjunction with chemical injection method. Acta Physica Sinica, 2007, 56(11): 6727-6735. doi: 10.7498/aps.56.6727
[20]	Qiao Yong-Hong, Wang Shao-Qing. Molecular dynamics studies on vacancy-interstitial annihilation in silicon. Acta Physica Sinica, 2005, 54(10): 4827-4835. doi: 10.7498/aps.54.4827

Catalog

Vol. 68, Issue 1 - 2019-01-05

Metrics

Abstract views: 7507
PDF Downloads: 237
Cited By: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

Search

Article

留言板