Workshop on Water at Biological
Interfaces
Hangzhou Water08
Shanghai Institute of Applied Physics
Oct. 27-28, 2008, Hangzhou, China
2008-10-27~2008-10-28
Workshop on Water at Biological
Interfaces
CONTENTS
1. Overview
2. Committee
3. Schedule of Lectures
4. Abstract of Lectures
1. Overview of the Scientific Program:
Date\time
26th Oct.
Sunday
27th Oct.
Monday
28th Oct.
Thursday
Morning
Noon
Opening
Session
(8:30~9:00)
Session 1
(9:00~12:10)
Lunch
(12:30~
13:30)
Session 3
(9:00~12:15)
Afternoon
Registration
(9:00-20:00)
Lunch
(12:30~
13:30)
Session 2
(14:00~18:30)
Session 4
(14:00~17:00)
Evening
Dinner
(18:30~20:00)
Dinner
(18:30~20:00)
2. Committee
Chair: Philip Ball
Co-chair: Haiping Fang
Scientific secretary: Shengfu Chen, Xiaoling Lei
Organizing Committee
1. Xiaowei Tang, Zhejiang University, China
2. Zhongcan Ouyang, Institute of Physics, CAS, China
3. Enge Wang, Institute of Physics, CAS, China
4. Lei Jiang, Institute of Chemistry, CAS, China
5. Ruhong Zhou, IBM Watson and Columbia University, USA
6. Jinghua Guo, Lawrence Berkeley National Laboratory, USA
7. Jichen Li, University of Manchester, UK
8. Yuhong Xu, Shanghai Jiao Tong University, China
9. Jun Hu, Shanghai Institute of Applied Physics, CAS, China
10. Fengshou Zhang, Beijing Normal University, China
11. Shengfu Chen, Zhejiang University, China
12. Gang Pan, State Key Laboratory of Environment Aquatic Chemistry,
CAS, China
13. Shaoping Deng, Zhejiang Gongshang University, China
14. Philip Ball, Nature, 4-6 Crinan Street, London N1 9XW, U.K
15. Haiping Fang, Shanghai Institute of Applied Physics, CAS, Shanghai
3. Schedule of Lectures
Data/
Time
26th Oct.
Sunday
27th Oct.
Monday
28th Oct.
Thursday
Morning
Noon
Afternoon
Evening
Registration(10:00-20:00)
Opening Session
Philip Ball(8:30~8:40)
Jun Hu(8:40~8:45)
Zhejiang University(8:45~8：
50)
Session 1
Lunch
Philip Ball(8:50~9:30)
(12:30~1
Coffee Break (9:30~9:50)
3:30)
Jiang Lei (9:50~10:30)
Sotiris Xantheas
(10:30~11:10)
Shengfu Chen(11:10~11:40)
Yuhong Xu (11:40~12:10)
Session 3
Jichen Li (9:00~9:40)
Jinghua Guo (9:40~10:20)
Coffee Break (10:20~10:35)
Jianzhong Wu
(10:35~11:15)
Yuguang Mu (11:15~11:45)
Jianxing Song (11:45~12:15)
Lunch
(12:30~1
3:30)
Session 2
Bertil Halle (14:00~14:40)
Ruhong Zhou (14:40~15:20)
Alenka Luzar (15:20~16:00)
Coffee Break (16:00~16:20)
Fengshou Zhang (16:20~16:50)
Jeremy England (16:50~17:30)
Xiaojing Gong (17:30~17:50)
Peng Xiu (17:50~18:10)
Discussion Session(18:10~18:30)
Session 4
Shaoping Deng (14:00~14:30)
Guanghong Wei (14:30~15:00)
Wei Gu (15:00~15:15)
Hai Li (15:15~15:30)
Fengyu Li (15:30~15:45)
Haiping Fang (15:45~16:015)
Discussion Session(16:15~17:00)
Dinner
(18:30~
20:00)
Dinner
(18:30~
20:00)
October 27, Monday
Morning: Opening session (8:30~9:00)
Philip Ball(8:30~8:40)
Jun Hu(8:40~8:45)
Some one from Zhejiang University(8:45~8:50)
Session #1:
Chair:?
Philip Ball (9:00~9:40)
Water in Molecular and Cell Biology
Coffee break (9:40~9:50)
Jiang Lei (9:50~10:30)
Design and Creation of Bioinspired Surfaces with Special Wettability
Sotiris Xantheas (10:30~11:10)
Development of an ab-initio based force field for water: Structural,
Thermodynamic and Spectral properties of water clusters, clathrate hydrates,
liquid water and ice
Shengfu Chen(11:10~11:40)
Yuhong Xu (11:40~12:10)
Afternoon: Session #2
Chair?
Bertil Halle (14:00~14:40)
Water-Biomolecule Interactions and Dynamics Studied by Magnetic Relaxation
Dispersion
Ruhong Zhou (14:40~15:20)
Dewetting and Hydrophobic Interaction in Physical and Biological Systems
Alenka Luzar (15:20~16:00)
Coffee break (16:00~16:20)
Fengshou Zhang (16:20~16:50)
Jeremy England (16:50~17:30)
Confined Water, Hydrophobicity, and Protein Stability In vitro and In vivo
Xiaojing Gong (17:30~17:50)
Molecular water pump driven by charges inspired by the structure of aquaporins
Peng Xiu (17:50~18:10)
Manipulating Biomolecules with Aqueous Liquids Confined within Single-walled
Nanotubes
Discussion Session(18:10~18:30)
October 28, Thursday
Morning: Session #3:
Chair?
Jichen Li (9:00~9:40)
Inelastic Neutron Scattering Studies of the structure and dynamics of Water
around DNA/proteins, amino acids and biopolymers
Jinghua Guo (9:40~10:20)
The molecular interfacial interactions in molecular liquids probed by soft-x-ray
spectroscopy
Coffee Break (10:20~10:35)
Jianzhong Wu (10:35~11:15)
Where to find a good molecular model for water?
Yuguang Mu (11:15~11:45)
Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between
DNA Molecules
Jianxing Song (11:45~12:15)
Revealing the Full Spectrum of Protein States in the Pure Water
Afternoon Session #4:
Chair?
Shaoping Deng (14:00~14:30)
Guanghong Wei (14:30~15:00)
Free energy landscape of trans- and cis-K3 peptides in explicit water
Wei Gu (15:00~15:15)
Role of interfacial water in protein-protein and protein-proton association
Hai Li (15:15~15:30)
Unconventional Self-Assembly of Peptides in Ambient Water Nanofilm on Mica
Surface
Fengyu Li (15:30~15:45)
Water clusters within nanoscale confinements from first-principles simulations
Haiping Fang (15:45~16:015)
Water channel gating of nanometer dimensions
Coffee break (16:00~16:15)
Discussion Session(16:15~17:00)
Titles of talks
4.
List:
1. Philip Ball
2. Jiang Lei
Water in Molecular and Cell Biology
Design and Creation of Bioinspired Surfaces with Special
Wettability
3. Sotiris Xantheas Development of an ab-initio based force field for water:
Structural, Thermodynamic and Spectral properties of water
clusters, clathrate hydrates, liquid water and ice
4. Shengfu Chen
5. Yuhong Xu
6. Bertil Halle
Water-Biomolecule Interactions and Dynamics Studied by
Magnetic Relaxation Dispersion
7. Ruhong Zhou
Dewetting and Hydrophobic Interaction in Physical and
Biological Systems
8. Alenka Luzar
9. Fengshou Zhang The solvation of NaCl and transition of DNA conformation
in model water solvent
10. Jeremy England Confined Water, Hydrophobicity, and Protein Stability In
vitro and In vivo
11. Xiaojing Gong Molecular water pump driven by charges inspired by the
structure of aquaporins.
12. Peng Xiu
Manipulating Biomolecules with Aqueous Liquids Confined
within Single-walled Nanotubes
13. Jichen Li
Inelastic Neutron Scattering Studies of the structure and
dynamics of Water around DNA/proteins, amino acids and
biopolymers
14. Jinghua Guo
The molecular interfacial interactions in molecular liquids
probed by soft-x-ray spectroscopy
15. Jianzhong Wu
Where to find a good molecular model for water?
16. Yuguang Mu
Molecular Dynamics Simulation of Multivalent-Ion Mediated
Attraction between DNA Molecules
17. Jianxing Song
Reveling the Full-spectrum of the Protein States in the Pure
Water
18. Shaoping Deng
19. Guanghong Wei Free energy landscape of trans- and cis-K3 peptides in
explicit water
20. Wei Gu
Role of interfacial water in protein-protein and protein-proton
association
21. Hai Li
Unconventional Self-Assembly of Peptides in Ambient Water
Nanofilm on Mica Surface
22. Fengyu
Li
23. Haiping Fang
Water clusters within nanoscale confinements from
first-principles simulations
Water channel gating of nanometer dimensions
Session #1：
1.1.1.
Water in Molecular and Cell Biology
Philip Ball
Nature, 4-6 Crinan St, London N1 9XW, UK
email: p.ball@nature.com
Biologists have long regarded water essentially as the canvas on which life’s molecular
components are arrayed, and have assumed that the liquid does little more than temper or
moderate the basic physicochemical interactions responsible for cellular activity. It has become
increasingly clear, however, that water is not simply ‘life’s solvent’, but is a substance that actively
engages and interacts with biomolecules in complex, subtle and essential ways. Water of hydration,
around both hydrophilic and hydrophobic entities, constitutes a malleable and responsive
‘component’ of biological macromolecules such as proteins and DNA, extending their range of
interactions with other molecules. The structure and dynamics of this hydration shell seems to feed
back onto those aspects of the proteins themselves, so that biological function depends on a
delicate interplay between what we have previously regarded as distinct entities: the molecule and
its environment. Many proteins make use of bound water molecules as functional units to mediate
interactions with other proteins or with substrate molecules, or to transport protons rapidly to
locations buried inside the protein.
In view of the many studies showing that water plays an active role in the molecular-scale
structure and function of the cell, it is time for water to claim its place as a genuine biomolecule. I
will outline the case for adopting this perspective. My aim is that this overview will provide a
basis for assessing water’s often-alleged ‘uniqueness’ to life. With this in mind, I shall try to
highlight the distinctions between generic and specific behaviours of biological water. I will also
point to some of the many questions that remain about the way water behaves structurally and
dynamically in the cell.
P. Ball,
Chem. Rev. 108, 74-108 (2008).
1.1.2.
Design and Creation of Bioinspired Surfaces with Special Wettability
Lei Jiang
Center of Molecular Sciences, Institute of Chemistry,
Chinese Academy of Sciences, Beijing 100190, China
Tel: 010-82621396 Fax: 010-82627566
e-mail: jianglei@iccas.ac.cn
Bio-inspired smart materials should be a “live” material with various functions like organism in
nature, they must have three essential elements as sense, drive and control. Our recent studies are
focused on the design and fabrication of bio-inspired surfaces with special wettability based on
these ideas. The studies on lotus and rice leaves reveal that a super-hydrophobic surface with both
a large CA and small sliding angle needs the cooperation of micro- and nanostructures, and the
arrangement of the microstructures on this surface can influence the way a water droplet tends to
move. Considering the arrangement of the micro- and nanostructures, the surface structures of the
water-strider’s legs were studied in detail. These results from the natural world provide a guide for
constructing artificial super-hydrophobic surfaces and designing surfaces with controllable
wettability. Accordingly, super-hydrophobic surfaces of aligned carbon nanotube films, aligned
polymer nanofibers and differently patterned aligned carbon nanotube films have been fabricated.
The large scale fabrications of super-hydrophobic polymer surfaces have been developed by
modification of the traditional template method, the adoption of one-step coating and
electrohydrodynamic processes respectively. Many of the methods had been applied in making
superhydrophobic films with multi-functional properties, such as structural colored, transparent
and/or conductive superhydrophobic films. Under certain circumstances, a surface wettability can
switch between superhydrophilicity and superhydrophobicity, just like in Chinese ancient Taiji
philosophy that “Yin” and “Yang”, the two opposing fundamental properties of nature, are
switchable. The cooperation between surface micro- and nanostructures and surface modification
of poly (N-isopropylacrylamide) gave reversible switching between superhydrophilicity and
superhydrophobicity in a narrow temperature range of about 10 °C. By grafting the copolymer of
temperature-sensitive and pH-sensitive components on the surface, a dual-responsive surface that
can be controlled by either or both of temperature and pH was fabricated. Besides the organic
surfaces, a series of inorganic switchers were also made in our lab. UV light stimulated transition
between superhydrophobic and superhydrophilic by aligned ZnO, TiO2, and SnO2 films are
successfully prepared respectively. In addition, a dual-responsive WO3 film with controlled
wetting and Photochromism was obtained by an inexpensive and simple electrochemical
deposition process. These studies have great application potentials in the fields of integrated
micro-electronic devices, microfluidic control, trace bioanalysis and smart functional windows,
etc..
Selected Publications:
1. Xuefeng Gao, Lei Jiang, Water-repellent legs of water striders, Nature, 2004, 432, 36.
2. Xinjian Feng, Lei Jiang, Design and Creation of Super-Wetting/Dewetting Surfaces, Adv. Mater., 2006, 18,
3063-3078.
3. Taolei Sun, Lin Feng, Xuefeng Gao, and Lei Jiang,
Bioinspired Surfaces with Special Wettability, Accounts of Chemical Research, 2005, 38, 644-652.
4. Lin Feng, Shuhong Li, Yingshun Li, Huanjun Li, Lingjuan Zhang, Jin Zhai, Yanlin Song, Biqian Liu, Lei Jiang,
Daoben Zhu,
Super-hydrophobic Surfaces: From Natural to Artificial, Adv. Mater., 2002, 14(24), 1857-1860.
1.1.3.
Development of an ab-initio based force field for water:
Structural, Thermodynamic and Spectral properties of water clusters, clathrate
hydrates, liquid water and ice#
Sotiris S. Xantheas
Chemical & Materials Sciences Division, Pacific Northwest National Laboratory
902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, WA 99352, USA
We present the development of a new flexible, all-atom polarizable, transferable classical
interaction potential for water [1-5], which is based on the results of high-level electronic structure
calculations of water clusters. The new model is based on smeared Coulombic, dipole-dipole
and van der Waals interactions. The total energy of a collection of water molecules is cast as the
sum of intramolecular terms, interactions between pairs of molecules and non-additive many body
terms. For the intramolecular part we utilize a potential energy surface (PES) and dipole moment
surface (DMS) obtained from high level electronic structure calculations coupled to a novel
scheme that allows for the intramonomer charge redistribution due to the change of the molecular
geometry. This DMS is further altered in order to describe the qualitatively different asymptotic
behavior upon elongation of the OH bond in condensed aqueous environments. Interactions
between pairs of molecules are parametrized from selected “chemically important” minimum
energy paths of the water dimer PES, which are obtained as a function of the O-O distance. The
many-body non-additive terms are assumed to be caused exclusively by induction and are
modeled using atom-centered dipoles, which are determined iteratively via a self-consistent
scheme. The interaction potential represents an attempt to approximate the Born-Oppenheimer
PES, it is suitable for quantum rather than classical statistical mechanical simulations and as such
it is transferable across different environments that are associated with different zero-point
energies. We will present results of converged nuclear quantum statistical simulations with the
new potential ranging from the structures and binding energies of water clusters up to n=22,
calculation of the second virial coefficient as well as structural, thermodynamic, transport and
spectral properties of liquid water and ice.
1. C. J. Burnham and S. S. Xantheas, Journal of Chemical Physics 116, 1479 (2002).
2. C. J. Burnham and S. S. Xantheas, Journal of Chemical Physics 116, 1500 (2002).
3. C. J. Burnham and S. S. Xantheas, Journal of Chemical Physics 116, 5115 (2002).
4. G. S. Fanourgakis and S. S. Xantheas, Journal of Physical Chemistry A 110, 4100 (2006).
5. G. S. Fanourgakis and S. S. Xantheas, Journal of Chemical Physics 128, 074506 (2008).
# This work was supported by the Division of Chemical Sciences, Geosciences and Biosciences,
Office of Science, US Department of Energy. Battelle operates the Pacific Northwest National
Laboratory for the US Department of Energy.
1.1.4.
Shenfu Chen
1.1.5.
Yuhong Xu
Session #2：
1.2.1．
Water-Biomolecule Interactions and Dynamics Studied
by Magnetic Relaxation Dispersion
Bertil Halle
Lund University, Sweden
The frequency dependence of the nuclear spin relaxation rates of the water nuclides 2H and 17O,
known as the magnetic relaxation dispersion (MRD), can be used to monitor the single-particle
dynamics of water molecules interacting with biomolecules. We have used the MRD method to
study water dynamics in the hydration layer at biomolecule-water interfaces in dilute solutions and
in living bacterial cells, and to characterize water molecules and ions buried in internal cavities in
proteins and nucleic acids. The MRD method can detect individual internal water molecules in the
presence of a 105-fold excess of bulk water and, by containing the dilute aqueous solution in
nonperturbing picoliter emulsion droplets, temperatures down to –35°C can be accessed without
cryosolvent.
After a brief introduction to the method, this talk will present the results of several recent MRD
studies of water interacting with the external and internal surfaces of proteins and nucleic acids in
vitro and in vivo, including the role of water in hydrophobic recognition and protein folding.
References
C. Mattea, J. Qvist & B. Halle (2008) Dynamics at the protein-water interface from 17O spin
relaxation in deeply supercooled solutions. Biophys J 95, 2951–2963.
M. Davidovic, C. Mattea, J. Qvist & B. Halle (2008) Protein cold denaturation as seen from the
solvent. JACS, submitted.
E. Persson & B. Halle (2008) Nanosecond to microsecond protein dynamics probed by magnetic
relaxation dispersion of buried water molecules. JACS 130, 1774–1787.
J. Qvist, M. Davidovic, D. Hamelberg & B. Halle (2008) A dry ligand-binding cavity in a solvated
protein. PNAS 105, 6296–6301.
E. Persson & B. Halle (2008) Cell water dynamics on multiple time scales. PNAS 105,
6266–6271.
1.2.2.
Dewetting and Hydrophobic Interaction in Physical and Biological Systems
Ruhong Zhou
IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598
Department of Chemistry, Columbia University, New York, NY 10027
Hydrophobicity manifests itself differently on large and small length scales. In this talk, I will go
over some of our recent works on large scale (>1nm) hydrophobicity, particularly dewetting
transitions, of confined water in both physical and biological systems, such as superhydrophobic
fluorocarbon plate collapse, water nanopore gating, protein complex folding, and protein-ligand
binding. This nanoscale dewetting transition, although occurring at microscopic level, is
reminiscent of the macroscopic first order phase transition from liquid to vapor. I will also go
over related macroscopic theories, molecular simulations, and recent experiments pertaining to
large scale hydrophobicity in the hope of clarifying some of the critical issues.
1.2.3.
Alenka Luzar
1.2.4.
The solvation of NaCl and transition of DNA conformation
in model water solvent
Feng-Shou Zhang1,2,3
1
College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875,
China
2
3
Beijing Radiation Center, Beijing 100875, China
Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of
Lanzhou, Lanzhou 730000, China
E-mail: fszhang@bnu.edu.cn
WWW: http://lenp.bnu.edu.cn/mse/zhangfs.htm
As the most important natural solvent, water is the basic matter for life on the earth and plays a
very crucial role in our living and production. The research on the prosperities of water is helpful
for us to understand and take advantage of the natural resources [1-12]. Based on the established
water models, we design several kinds of model solvents with different hydrogen bonding abilities,
local structures and molecular polarities by changing the potential parameters. The solvation
dynamics of NaCl in the solvent of varying hydrogen bonding abilities and local structures are
systematically studied. The analyses of the micro-structures and dynamical behaviors of solvent
and ion solute indicate that the ions are most ideally hydrated and dissolved in natural water. In
solvent with both increased and decreased hydrogen bond strength, they are more inclined to be in
contact and form ion clusters of different sizes [13,14]. We also study the DNA structure changes
in the solvent with different molecular polarities. When the polarity of the solvent molecule
decreases, from over-polarized to less-polarized, DNA experiences the conformational transitions
of: Constrained B form  (A-B)mix A form. We demonstrate that the reason of these
structure changes is the competition between hydration and direct cation-coupling to the free
oxygen atoms in the phosphate groups on DNA backbones[15].
[1] P. Ball, Water and life: seeking the solution, Nature 436 (2005)1084
[2] P. Ball, Water - an enduring mystery, Nature 452 (2008)291
[3] P. Ball, Water as an Active Constituent in Cell Biology, Chem. Rev. 108 (2008)74
[4] X.J. Gong, J.Y. Li, H.J. Lu, R.Z. Wan, J.C. Li, J. Hu, H.P. Fang, A charge-driven molecular
water pump, Nature Nanotechnology 2 (2007) 709
[5] M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids, Clarendon, Oxford, 1987
[6] F.S. Zhang and R.M. Lynden-Bell, Solvent-induced symmetry breaking, Phys. Rev. Lett. 90
(2003)185505
[7] F.S. Zhang and R.M. Lynden-Bell, Temperature and solvent dependence of vibrational
relaxation of triodide: a simulation study, J. Chem. Phys.119 (2003)6119
[8] F.S. Zhang and R.M. Lynden-Bell, Pure vibrational dephasing of triiodide in liquids and
glasses, Mod. Phys. Lett. A18 (2003) 406-409.
[9] F.S. Zhang and R.M. Lynden-Bell, A simulation study of vibrational relaxation of I3- in liquids,
Molec. Phys. 101 (2003) 1641.
[10] R.M. Lynden-Bell and F.S. Zhang, Using Simulations to study vibrational relaxation of
molecules in liquids, in “Novel approaches to the structure and dynamics of liquids;
experiments, theories and simulations, Book Series: NATO SCIENCES SERIES: II:
Mathematics, Physics and Chemistry: Volume 133.” ed J.Samios and V.A.Durov (2004) 323,
Kluwer Academic Publishers
[11] F.S. Zhang and R.M. Lynden-Bell, Solvent-induced symmetry breaking: varying solvent
strength, Phys. Rev. E 71 (2005) 021502
[12] F.S. Zhang and R.M. Lynden-Bell, Interactions of triiodide cluster ion with solvents, Eur.
Phys. J. D34 (2005) 129
[13] B. Gu, F.S. Zhang. Z. P. Wang, and H. Y. Zhou, The solvation of NaCl in model water with
different hydrogen bond strength, J. Chem. Phys. (2008), in prerss
[14] B. Gu, F.S. Zhang. Z. P. Wang, and H. Y. Zhou, The non-ideal solvation of NaCl in solvent: a
simulation study, Molec. Phys. 106 (2008)1047
[15] B. Gu, F.S. Zhang. Z. P. Wang, and H. Y. Zhou, Solvent-Induced DNA conformational
transition, Phys. Rev. Lett. 100 (2008)088104
1.2.5.
Confined Water, Hydrophobicity, and Protein Stability In vitro and In vivo
Jeremy England
The shape that a polypeptide chain adopts is not determined by its amino acid sequence alone, but
rather by the interaction between that sequence and the solvent environment the chain finds itself
in. This point is amply illustrated by the fact that natively-folded proteins that are stable in buffer
usually unfold when chemical denaturants are introduced into the solution. Here, we use molecular
dynamics simulations and analytical theory to study how the hydrophobic effect, a crucial driving
force for protein folding, may be modulated in different solvent environments. By studying the
phenomenon of dewetting between hydrophobic plates in simulation, we find that the chemical
denaturants urea and guanidinium chloride attenuate the hydrophobic effect relative to its strength
in pure bulk water. In contrast, we argue based on theoretical grounds that the interior cavity of a
closed GroEL-ES chaperonin barrel should provide a local solvent environment in which the
hydrophobic effect, and therefore an encapsulated chaperonin substrate protein's tendency to fold,
is enhanced relative to bulk. This argument leads us to put forward the prediction that a
chaperonin's ability to accelerate folding should be correlated with its interior cavity's affinity for
water, a prediction that we verify by comparing the results of simulations of GroEL mutants to
experimentally measured folding rates.
1.2.6.
Xiaojing Gong
1.2.7.
Peng Xiu
Session #3:
1.3.1.
Inelastic Neutron Scattering Studies of the structure and dynamics of Water
around DNA/proteins, amino acids and biopolymers
Jichen Li
Department of Physics and Astronomy, the University of Manchester,
Manchester, M60 1QD, UK
Experimental investigations of water around nucleic acids and proteins are traditionally difficult.
The use of diffraction (X-ray or neutron) techniques is restricted for this type of study, because
crystalline specimens require purified components that are far removed from their normal
physiological environment. Moreover X-rays interact weakly with protons making X-ray
diffraction unsuitable for examining the structures of water (except for the few protein or nucleic
acid crystals that diffract beyond 0.1 nm resolution). Neutron scattering, on the other hand, has
the ability to ‘see’ proton positions. However the complex structures of DNA/proteins and the
conformational arrangements of water molecules around them make it very hard to gain a clear
picture of the spatial arrangements as often only averaged (time and molecule) positions are given.
In addition, neutron fluxes are typically weak compared to X-ray sources, and this necessitates
both long collection times and extremely large crystals. However, using vibrational spectroscopy
(including neutron, IR and Raman), we can determine the local structures of water in biological
environments by comparing the spectra of known structures, such as exotic phases of ice [1] with
those of our biological systems. We can thus deduce the interactions between water molecules and
DNA, proteins and biopolymers.
Our recent studies of water in DNA, proteins and biopolymers shed new light towards the
understanding of the structure and dynamics of water in the biological environments and the roles
of water in biological environment. However, the complexity of proteins and biopolymers [2,3]
(consisting of hundreds of amino acids) has so far proven too difficult for us to make a more
precise understanding of the relationship between the water structures of hydration sites on the
biomolecules. In order to make further progress in this field, we have studied the systems of water
and amino acids which is the basic building block of proteins and small segments of peptides
under different extreme conditions. These molecules exhibit the following properties, small, well
characterised and having known interaction sites with water, these systems provide an excellent
opportunity for us to study their hydration states. By comparising with the known states of water,
the neutron scattering spectra show new insight towards our understanding of the interaction
between water and the amino acids peptides [4]. Based on these spectra, we also performed ab
initio simulations which would provide the necessary assignment for the vibrational modes seen in
the measured INS spectra.
1. J.C. Li, J. Chem. Phys. 105 (1996) 6733-6755.
2. Stuart V. Ruffle, Ilias Michalarias, Jichen Li and Robert C. Ford, J. Amer. Chem. Soc. 124 (2002)
565-569.
3. Robert C. Ford, Stuart V. Ruffle, Ilias Michalarias, Ilir Beta, Aline Miller, and Jichen Li, J. Amer.
Chem. Soc. 126 (2004) 4682-4688.
4. Ying Zhang, Peng Zhang, Robert C Ford, Shenghao Han and Jichen Li, J. Phys. Chem. B 109
(2005) 17784-17786.
1.3.2.
The molecular interfacial interactions in molecular liquids probed
by soft-x-ray spectroscopy
Jinghua Guo
Advanced Light Source, Lawrence Berkeley National Laboratory,
Berkeley, CA 94720
Many vital chemical and biological processes take place in aqueous solutions. Understanding and
begin able to determine the mixing properties of different liquids is of great importance. Small
molecules can be studied in great detail in the gaseous phase, where molecular interactions can be
neglected, and consequently both their geometric structure and electronic structure are often well
known. However, when the molecules interact in the liquid phase, our knowledge about these
fundamental properties is very limited. Not only does the arrangement of the molecules change on
a fast time scale: the geometry and the electronic structure of the molecules themselves vary, i.e.,
the properties of the individual molecules are constantly changing. Thus, from this perspective it
is not surprising that there is still much to learn about common and simple liquids.
We have used synchrotron based soft-x-ray spectroscopy to elucidate the structure of liquid water
and the simplest alcohol, methanol. The soft-x-ray absorption and emission spectra reveal new
details of their complex hydrogen bonded networks. We have found that pure liquid methanol
forms rings and chains with 6 or 8 molecules, which sheds light on a forty-year controversy over
the molecular structure in liquid methanol. When mixing alcohol and water it is well-known that
the entropy does not increase as expected for ideal solutions. Our results show that the liquids mix
very little on the microscopic level. Instead, new ordered structures are formed, in which both
water and methanol molecules take part. The study illustrates how soft-x-ray spectroscopy can be
used to elucidate the structure of hydrogen-bonded solutions. We believe that this technique has
great general potential to provide new and valuable information in the quest for the microscopic
origin of the properties of liquids and solutions.
1.3.3.
Where to find a good molecular model for water?
Jianzhong Wu
Department of Chemical and Environmental Engineering, University of
California, Riverside, CA 92521, USA
Liquid water is unique primarily due to the formation of a hydrogen-bonding network that is
sensitive to the positions of oxygen and hydrogen atoms at a fraction of an Angstrom. The
multi-body effect seems too subtle to be captured either by Newton’s equation or by
quantum-mechanical calculations. However, reliable experimental data are available for the
solvation free energy of individual solute molecules and for the distribution of water molecules in
the solvation layer. In this talk, I will illustrate how a simple thermodynamic analysis can provide
insights on organization of water molecules near a hydrophobic solute and on the water-mediated
interactions. The thermodynamic analysis may be used as guidance towards development of a
faithful molecular model for aqueous systems.
1.3.4.
Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction
between DNA Molecules
Yuguang Mu
All atom molecular dynamics simulations with explicit water were done to study the interaction
between two parallel double-stranded DNA molecules in the presence of the multivalent
counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The
inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive
force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are
simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short
on the order of a few nanoseconds.
Reference:
Liang Dai, Yuguang Mu, Lars Nordenskiold, and Johan van der Maarel,
Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules
Phys. Rev. Lett. 100 (2008) 118301.
1.3.5.
Reveling the Full-spectrum of the Protein States in the Pure Water
Jianxing Song
National Univeristy of Singapore, Singapore
Proteins are important functional players that implement the most difficult but essential tasks in
living cells. Proteins fold into the well-folded native state from highly unfolded states via a large
spectrum of partially-folded intermediates (1-2). Unusually the intermediates are prone to
aggregation and also many proteins have been found to be not soluble and refoldable in buffer
systems. Previously no general method is available to solubilize these proteins without addition
of detergents or/and denaturants.
Very unexpectedly, we recently discovered that ~30 buffer-insoluble proteins we have could be
easily solubilized in water at high concentrations. This discovery offers us an unprecedented
possibility to characterize them by circular dichroism (CD) and NMR spectroscopy (3-6). The
results lead to the classification of the insoluble proteins into three groups which are all absent of a
tight tertiary packing. Therefore, we propose that insoluble proteins may lack intrinsic ability to
reach or/and to maintain a well-packed conformation, and thus are trapped in partially-folded
states with many hydrophobic side chains exposed to the bulk solvent. As such, a very low ionic
strength is sufficient to screen out intrinsic repulsive interactions (such as to reduce or disrupt the
hydration shell which is the largest at zero salt concentration) and, consequently, allow the
hydrophobic clustering/aggregation to occur. Interestingly, on Earth, almost every activity in
living cells occurs in water-based media, mostly with the presence of salt ions. Marvelously
enough, however, it appears that when proteins were originally selected to be functional players
for life on Earth, they might have been offered the potential to manifest their full spectrum of
structural states, ranging from the denatured to native states, by utilizing intrinsic repulsive
interactions to suppress attractive hydrophobic clustering in the pure water.
Our discovery not only sheds the first light on previously unknown regimes associated with
proteins, but also provides a powerful tool for protein folding and design investigations (7-8).
References
1. Song J*, Jamin N, Gilquin B, Vita C, Menez A (1999) A gradual disruption of tight side-chain
packing Nature Struct. Biol. 6, 129-34
2. Wei Z and Song J* (2005) Molecular mechanism underlying the thermal stability and
pH-Induced unfolding of CHABII J. Mol. Biol. 348, 205-218
3. Li M, Liu J, Ran X, Fang M, Shi J, Qin H, Goh J-M, and Song J* (2006) Resurrecting
Abandoned Proteins with Pure Water: CD and NMR Studies of Protein Fragments Solubilized in
Salt-Free Water. Biophys. J. 91:4201-4209
4. Li M, Liu J and Song J* (2006) Nogo goes in the pure water: solution structure of Nogo-60
and design of the structured and buffer-soluble Nogo-54 for enhancing CNS regeneration Protein
Sci. 15, 1835-41.
5. Ran X, Qin H, Liu J, Fan JS, Shi J and Song J* (2008) NMR structure and dynamics of
human ephrin-B2 ectodomain: The functionally critical C-D and G-H loops are highly dynamic in
solution. Proteins. 72, 1019–1029.
6. Li M and Song J* (2007) Nogo-B receptor possesses an intrinsically-unstructured
ectodomain and a partially-folded cytoplasmic domain. Biochem Biophys Res Commun. 360,
128-34
7. Li M, Li Y, Liao X, Liu J, Qin H, Xiao Z and Song J* (2008) Rational Design, Solution
Conformation and Identification of Functional Residues of the Soluble and Structured Nogo-54,
which Mimics Nogo-66 in Inhibiting the CNS Neurite Outgrowth Biochem Biophys Res Commun.
373, 498-503.
8. Liu J and Song J* (2008) NMR Evidence for Forming Highly-Populated Helical
Conformations in the Partially-Folded hNck2 SH3 Domain Biophys. J. PMID: 18599634.
Session #4:
1.4.1.
Shaoping Deng
1.4.2.
Free energy landscape of trans- and cis-K3 peptides in explicit water
Guanghong Wei
Physics Department, Fudan University, Shanghai, 200433, China
Solid-state NMR study shows that the 22-residue K3 peptide (Ser20-Lys41) from
2-microglobulin (2m) adopts a -strand-loop--strand conformation in its fibril state [1].
Residue Pro32 has a trans conformation in the fibril state of the peptide[1], while it adopts a cis
conformation in the native state of full-length 2m [2]. To get insights into the structural
properties of the K3 peptide, and determine whether the strand-loop-strand conformation is
encoded at the monomeric level, we run all-atom explicit solvent replica exchange molecular
dynamics on both the cis and trans variants. Our simulations show that the conformational space
of the trans and cis-K3 peptides is very different, with 1% of the sampled conformations in
common at room temperature. In addition, both variants display only 0.3–0.5% of the
conformations with -strand-loop--strand character. This finding, compared to results on the
Alzheimer’s A peptide, suggests that the biases toward aggregation leading to the
-strand-loop--strand conformation in fibrils are peptide-dependent
References
[1] K. Iwata, T. Fujiwara, Y. Matsuki, H. Akutsu, S. Takahashi, H. Naiki, and Y. Goto. Proc. Natl.
Acad. Sci. USA. 103:18119–18124 (2006).
[2] G. Verdone, A. Corazza, P. Viglino, F. Pettirossi, S. Giorgetti, P.Mangione, A. Andreola, M.
Stoppini, V. Bellotti, and G. Esposito. Protein Sci. 11:487–499. (2002).
1.4.3.
Role of interfacial water in protein-protein and protein-proton association
Wei Gu
Center for Bioinformatics, Saarland University, D-66041 Saarbruecken,
Germany
Protein-protein association is a fundamental event that plays a central role in the regulation of
biological processes and in the development of many diseases. Previous experimental and
computational studies have provided information about the diffusion phase and the nature of the
intermediate complexes. However, our understanding of the transformation from the intermediate
complexes to the stereospecific complex, where the desolvation takes place, is still limited. We
have used extensive atomistic molecular dynamics simulations with explicit solvent to study the
binding of an SH3 domain with its binding partner as a general example for protein binding
mediated by modular protein domains [1]. The simulations showed a dual mechanism of binding
where the long range electrostatic interactions play an essential role in accelerating and guiding
the diffusion phase that leads to the formation of intermediate encounter complexes of electrostatic
nature stabilized by salt bridges. In the last steps of binding, hydrophobic dewetting is established
between the two hydrophobic interfaces. This decrease in the interfacial water density acts as a
driving force for the collapse of the interfaces and formation of the stereospecific complex.
Attracting protons from bulk solution and transferring them through biological membranes are the
main tasks of most trans-membrane proton pumps. By such a one-directional pumping, a proton
gradient is built up to serve as an energy source to synthesize the bio-energetic unit — ATP. As
many of the proton pumps transfer protons much faster than the random diffusion of proton in
bulk, clusters of negatively charged residues have been proposed as "proton collecting antenna" to
capture proton from bulk solution efficiently [2]. We found that water near the surface composed
of lipid membrane head groups and proton collecting antenna can transiently form tightly
connected water wires that allow ultra fast proton transfer within the "coulomb cage" of the proton
antenna. Once a proton "touches" one of these water wires, the increased chance of fast delivery of
this proton to the collecting site further accelerates the last step of proton capturing.
[1] Ahmad, M., Gu, W., and Helms, V. Mechanism of Fast Peptide Recognition by SH3 Domains.
Angew. Chem. Int. Ed. (in press)
[2] Gutman, M. and Nachliel, E. Time-resolved Dynamics of Proton Transfer in Proteinous
System. Annu. Rev. Phys. Chem. (1997) 48:329-56
1.4.4.
Unconventional Self-Assembly of Peptides in Ambient Water Nanofilm on Mica
Surface
Hai Li,† Feng Zhang,† Yi Zhang,† Ming Ye,†, ‡ Bo Zhou,†, ‡ Yu-Zhao Tang,§
Hai-Jun Yang,†, ‡ Mu-Yun Xie,†, ‡ Sheng-Fu Chen,** Jian-Hua He,† Hai-Ping
†Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai,
201800, China and ‡ Graduate School of the Chinese Academy of Sciences,
Beijing, 100049, China and §Bio-X Life Sciences Research Center, College of Life
Science and Biotechnology, Shanghai JiaoTong University, Shanghai, 200240,
China and ** Institute of Pharmaceutical Engineering, College of Materials
Science and Chemical Engineering, Zhejiang University, Zhejiang, 310027,
China and †† Shanghai Center for Systems Biomedicine, Shanghai, 200240,
China
E-mail: HUfanghaiping@sinap.ac.cnUH; HUjunhu22@hotmail.com
Self-assembling in nanoconfined environment usually leads to the formation of novel
materials not seen in bulk. Ambient water nanofilms on solid surface that confined
between the supporting substrate and the vapor/liquid interface usually show
properties very different from that in bulk, and play unique roles in many important
physical and chemical processes. Here, we report unexpected self-assembling of
peptides into novel one-dimensional epitaxial nanofilaments in ambient water
nanofilms on mica surface, based on “drying microcontact printing” and atomic force
microscopy imaging. The self-assembled peptides show a new type of “lying down”
epitaxial structure on the mica surface and are highly stable under a wide range of
humidity as compared to the instability of self-assembled structures in bulk. This
water nanofilm is important for the emerging fields of molecular environmental
sciences and surface biology and also has wide applications in both laboratory and
industry.
1.4.5.
Water clusters within nanoscale confinements from first-principles simulations
Lu Wang, Fengyu Li, Jijun Zhao*
Laboratory of Materials Modification by Laser, Electron, and Ion Beams, School
of Physics and Optoelectronic Technology and College of Advanced Science and
Technology, Dalian University of Technology, Dalian 116024, China
*
Corresponding author: E-mail: zhaojj@dlut.edu.cn; Phone: 0086-411-84709748; Fax:
0086-411-84706100.
Water molecules confined in the nanoscale environments is of great importance for understanding
many biological activities of macromolecules as well as for designing novel molecular devices.
Using first-principles density functional theory, we have systematically investigated two kinds of
model systems to mimic the water clusters confined in the nanoscale nonpolar and polar
confinements, namely, carbon fullerene cages [1] and finite single-walled carbon nanotubes. We
found that the water-host interaction is mainly of van der Waals type and can be reasonably
described by GGA-PW91 method. Weak coupling were found between the molecular orbitails
carbon nanotube and water molecules. Even through the interaction is weak, carbon hosts (i.e.,
both fullerene cage and nanotube) exhibit screening effect that significantly reduces the dipole
moments of the water clusters with regard to the vacuum values. Meanwhile, the nanoscale
confinements clearly affect the hydrogen bonded configuration of water clusters, for example,
water molecules form chains inside narrow carbon nanotube and form cage-like configurations
within fullerene cages. These hydrogen-bonded configurations of water clusters can be validated
by comparing the vibrational spectra from theoretical predictions and experimental measurements.
[1] Lu Wang, Jijun Zhao, Haiping Fang, Journal of Physical Chemistry C 112, 11779 (2008).
1.4.6.
Haiping Fang