What effects do salts have
on biopolymers?
.
Maxim V. Fedorov1, Ingrid Socorro1, Stephan Schumm2
and Jonathan M. Goodman1
1 Unilever
Centre for Molecular Science Informatics,
Department of Chemistry, University of Cambridge, Cambridge, UK
2 Unilever R&D Vlaardingen, Vlaardingen, The Netherlands
• Research:
Biopolymers interactions with salts in
water.
• Systems:
Water with salt and:
– Oligopeptides (3 - 21 amino acids)
– Bee toxin (mellitin; 27 amino acids)
• Methods:
Fully atomistic Molecular Dynamics
simulations
What effect do salts have on biopolymers?
Some of important processes are:
- biopolymer solubility
- biopolymer denaturation temperatures
- enzyme activity
- biopolymer swelling
- growth rates of bacteria
- stability of protein macroaggregates
Energetic optimization of mutual
hydrogen bonded networks
The water hydrogen bonded
network links secondary
structures within the protein
Water and cosolutes as ‘lubricants’ for protein folding.
Schematic potential energy funnel for
the folding of proteins without water:
many barriers to the preferred minimum
energy structure on the folding pathway
There are numerous local
minima that might trap the
protein in an inactive
three-dimensional
molecular conformation
Fully hydrated protein: the
potential energy landscape is
smoother
Salt effects on biopolymer shapes
D. Puett et al., JCP, 1967; H. Saito et al., Biopolymers, 1978; K. Zero & B.R. Ware, JCP, 1984;
Poly-L-Lysine, bulk water solution
Poly-L-Lysine, NaCl solution
Assembly of two oligopeptides in water
C. Muhle-Goll, et al., Biochemistry, 1994; P. Aymard, D. Durand & T. Nicolai, Int. J. Biol. Macromol.,1996
Self-assembly to very stable amyloids
M. V. Fedorov et al Phys. A, 2006
• Poly-L-Lysine (PLL), a-Helix
• Water solution (2300 water molecules)
• Water and salt (2300 water and a few dozen NaCl molecules)
Results: No Ions
R
A
N
D
O
M
C
O
I
L
Comparison of two systems
PLL: no ions
PLL: 0.50 M NaCl
Ramachandran density maps
0.50 M NaCl
Na+
H
E
L
I
X
Cl-
Three major effects of ions
• Electrostatic screening (Debye-Hückel effect)
• Specific interactions by ion-pair formation
(Electroselectivity effect)
• Salts affect water structure, which may
change the hydrophobic interactions
(Hofmeister effect)
Hofmeister Effect
In 1888 Hofmeister observed that protein solubilities are
influenced by the concentration and type of salts present.
Solubilities tend to follow the general order:
SO42- < F- < Cl- < Br- < I- < SCN- < ClO4precipitate,
stabilize
solubilize,
destabilize
Mg2+ < Na+ < K+ < Li+
Other phenomena to follow the Hofmeister series:
- water activity
- self-diffusion coefficient of water
- viscosity of salt solutions
- surface tension
- lipid solubility of monoanions
- polymer cloud points
- polymer swelling
- protein solubility
- protein denaturation temperatures
- degree of protein aggregation
- coacervate behaviour
- critical micellar concentration
- enzyme activity
- growth rates of bacteria
Electroselectivity (direct binding) effect
In 1990-1992 Goto and coworkers observed that conformation properties of some
polypeptide and proteins solubilities are influenced by the concentration and type
of 1:1 salts present following the electroselectivity series:
electroselectivity
I- < Br- < Cl- < F-
precipitate,
stabilize
solubilize,
destabilize
Hofmeister
F- < Cl- < Br- < IInverse order with compare to the Hofmeister series for monovalent anions.
Verification
• If the Debye-Huckel screening is important, the effect
of various ions will be determined only by the ionic
strength of solution
• If the electroselectivity is important, the effect of
different ions should follow the electroselectivity series
of the salts
• The importance of the Hofmeister effect can be
determined by comparing the different ions with the
Hofmeister series
System
•
•
•
•
•
•
•
•
•
•
•
Poly-L-Alanine 3 (PAA), a-Helix (-57,-47).
~1200 water molecules (TIP5P-E)
Li+, Na+, K+, Cs+ cations
F-, Cl-, Br-, I- anions.
OPLS/AA force-field
Periodic Boundary Conditions
Particle Mesh/Ewald electrostatics
BOX: 37 Å x 37 Å x 37 Å
Berendsen thermostat/barostat
GROMACS 3.3
Equilibration run: 27 ns, production run: 27 ns.
+
-
How long shall we simulate?
Sampled part V of the available volume Vmax (volume of the box without the excluded
volume of the tripeptide) visited be any of chlorine ions as a function of simulation
time. This demonstrates equilibration time >> 1 ns as required for chlorines to visit
any part of the box.
Molecular Surfaces
• Dotted line: Solvent
Accessible Surface
(SAS)
• Solid line: molecular
surface (MS)
• Shaded grey area:
van der Waals
surface
Water accessible area
Compact
conformations
Water accessible area
NaCl
NaBr
NaI
NaF
Ratio of compact conformations
WHY???
Electroselectivity (direct binding) effect
electroselectivity
I- < Br- < Cl- < F-
precipitate,
stabilize
solubilize,
destabilize
Hofmeister
F- < Cl- < Br- < IInverse order with compare to the Hofmeister series for monovalent anions.
Possible ways of interactions:
• Direct contacts:
+
-
• Shell – Shell contacts:
--
+
•
Site – water – Site contacts:
+
-
+
+
-
Direct Contact: fluorine anions
Shell-shell interactions.
Macroscopic Coulomb’s law doesn’t
work on the molecular level.
• Macro
q
U macro ( r ) 
 0r
Micro
q
U micro (r ) 
F (r ) 0 r
F(r) – dielectric permittivity (screening factor).
F (r )  1, r  
Visualization of the (a) electrostatic potential, (b) screening factor and (c) ion-hydrogen (- - -)
and ion-oxygen ( --- ) RDF, created by a single charge anion/ cation (of radii a =1 A ) as
functions of the distance from the surface of the sphere, R-a, which mimics the ion:.
MVF and A. A. Kornyshev, Mol. Phys., 2007, to be issued soon
Potential of Mean Force
Activation Energy
Structure & Dynamics
Peptide-water and ion-water PMFs
EIW
Peptide –ion PMFs
N-terminus
C-terminus
Peptide –ion PMFs
Side chain groups
Backbone groups
EPI
Preferential Interaction
Cosolutes will change the chemical potential of a protein in a cosolvent solution
compared to a pure solvent due to preferential interaction with or exclusion
from the protein interface.
Gtr  0
Gtr  0
transfer free energy:
The protein prefers to
be surrounded by
cosolvent molecules
Protein
solvent
Gtransfer   cosolvent

protein
protein
water
cosolvent
The transfer from pure
solvent to the cosolvent
solution in unfavourable.
The protein prefers to be
surrounded by solvent
molecules.
Protein
Specific interactions of
ions with polypeptide
charges
(local effects)
Preferential solvent / salt
interactions (bulk effects)
Conclusions
• Salt effects on biopolymer solutions can be
reproduced “in silico” using the fully atomistic
Molecular Dynamics simulations.
• Generally, ions contact biopolymers via an
intermediate water shell.
• We can distinguish between the Debye-Hückel,
Electroselectivity and Hofmeister effects for
salts
Financial Support
• Unilever R&D Vlaardingen
Acknowledgements
Robert Glen, Dmitry Nerukh ( Unilever Centre for Molecular Science
Informatics, University of Cambridge, UK);
Ruth Lynden-Bell (University of Belfast & University of Cambridge, UK);
Alexei A Kornyshev (Imperial College London, UK);
Gennady N Chuev (Institute of Experimental and Experimental Biophysics
of RAS, Pushchino Biological Centre, Russia & University of Edinburgh, UK).