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Permeation
of Membranes by Ribose and Its Diastereomers
Chenyu
Wei and Andrew Pohorille
It was recently found that ribose permeates membranes an order of
magnitude faster than its diastereomers arabinose and xylose
(Sacerdote, M. G.; Szostak, J. W. Proc. Natl. Acad. Sci. U.S.A. 2005,
102, 6004). On this basis it was hypothesized that differences in
membrane permeability to aldopentoses provide a mechanism for
preferential delivery of ribose to primitive cells for subsequent
selective incorporation into nucleotides and their polymers. However,
the origins of these unusually large differences have not been well
understood. We address this issue in molecular dynamics simulations
combined with free energy calculations. It is found that the free
energy of transferring ribose from water to the bilayer is lower by
1.5−2 kcal/mol than the barrier for transferring the other two
aldopentoses. The calculated and measured permeability coefficients are
in excellent agreement. The sugar structures that permeate the membrane
are β-pyranoses, with a possible contribution of the α-anomer for
arabinose. The furanoid form of ribose is not substantially involved in
permeation, even though it is non-negligibly populated in aqueous
solution. The differences in free energy of transfer between ribose and
arabinose or xylose are attributed, at least in part, to stronger
highly cooperative, intramolecular interactions between consecutive
exocyclic hydroxyl groups, which are stable in nonpolar media but rare
in water. Water/hexadecane partition coefficients of the sugars
obtained from separate molecular dynamics simulations correlate with
the calculated permeability coefficients, in qualitative agreement with
the Overton rule. The relevance of our calculations to understanding
the origins of life is discussed.
J. Am. Chem. Soc. 2009, 131(29), 10237-10245 |
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Building
a foundation for structure-based cellulosome design for cellulosic
ethanol: Insight into cohesin-dockerin complexation from computer
simulation
Jiancong
Xu, Michael F. Crowley, and Jeremy C. Smith
The organization and assembly of the cellulosome, an extracellular
multienzyme complex produced by anaerobic bacteria, is mediated by the
high-affinity interaction of cohesin domains from scaffolding proteins
with dockerins of cellulosomal enzymes. We have performed molecular
dynamics simulations and free energy calculations on both the wild type
(WT) and D39N mutant of the C. thermocellum Type I cohesin-dockerin
complex in aqueous solution. The D39N mutation has been experimentally
demonstrated to disrupt cohesin-dockerin binding. The present MD
simulations indicate that the substitution triggers significant protein
flexibility and causes a major change of the hydrogen-bonding network
in the recognition strips - the conserved loop regions previously
proposed to be involved in binding - through electrostatic and
salt-bridge interactions between beta-strands 3 and 5 of the cohesin
and alpha-helix 3 of the dockerin. The mutation-induced subtle
disturbance in the local hydrogen-bond network is accompanied by
conformational rearrangements of the protein side chains and bound
water molecules. Additional free energy perturbation calculations of
the D39N mutation provide differences in the cohesin-dockerin binding
energy, thus offering a direct, quantitative comparison with
experiments. The underlying molecular mechanism of cohesin-dockerin
complexation is further investigated through the free energy profile,
that is, potential of mean force (PMF) calculations of WT
cohesin-dockerin complex. The PMF shows a high-free energy barrier
against the dissociation and reveals a stepwise pattern involving both
the central -sheet interface and its adjacent solvent-exposed loop/turn
regions clustered at both ends of the beta-barrel structure.
Prot. Sci. 2009, 18(5), 949-959 |
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Inclusion
Mechanism of Steroid Drugs into β-Cyclodextrins. Insights from Free
Energy Calculations
Wensheng
Cai, Tingting Sun, Peng Liu, Christophe Chipot and Xueguang Shao
The inclusion of hydrocortisone, progesterone, and testosterone into
the cavity of β-cyclodextrin (β-CD) following two possible orientations
was investigated using molecular dynamics simulations and free-energy
calculations. The free-energy profiles that delineate the inclusion
process were determined using an adaptive biasing force. The present
results reveal that although the free-energy surfaces feature two local
minima corresponding to a partial and a complete inclusion, the former
mode is markedly preferred, irrespective of the orientation. Ranking
the propensity of the three steroidal molecules to associate with β-CD,
viz. progesterone > testosterone > hydrocortisone, is shown to be
in excellent agreement with experiment. This conclusion is further
supported by independent calculations relying on alchemical
transformations in conjunction with free energy perturbation, wherein
the relative binding free energy for the three steroids was estimated.
In addition, decomposition of the potentials of mean force into
free-energy contributions and significant decrease in the total
hydrophobic surface area suggest that by and large, van der Waals and
hydrophobic interactions constitute the main driving forces responsible
for the formation of the inclusion complexes. Analysis of their
structural features from the molecular dynamics trajectories brings to
light different hydrogen-bonding patterns that are characterized by
distinct dynamics and stabilities.
J. Phys. Chem. B 2009, Article ASAP |
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Building
up Nanotubes: Docking of “Janus” Cyclodextrins in Solution
Javier
Rodriguez, Rocío Semino and Daniel Laria
Using molecular dynamics experiments, we analyze the association of
“Janus” 6-amino-6-deoxy-2O-carboxymethyl-β-cyclodextrins (JCD) in
aqueous solutions. In JCD dimers, the free energy associated with the
primary-rim−secondary-rim docking shows a stable minimum of ~−45 kcal
mol−1. Trimers in solution are also remarkably stable,
exhibiting minimal distortions in their spatial and orientational
distributions. The resulting geometrical docking shows the incipient
characteristics of flexible nanotubes in solution, with eventual water
interchange between the central channel and the bulk at the junctions
between monomers. Structural and dynamical properties of the trapped
water filling the nanotube are dictated to a large exent by the charge
density at the rims.
J. Phys. Chem. B 2009, 113(5), 1241-1244 |
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Interactions
between amino acid side chains in cylindrical hydrophobic nanopores
with applications to peptide stability
S.
Vaitheeswaran and D. Thirumalai
Confinement effects on protein stability are relevant in a number of
biological applications ranging from encapsulation in the cylindrical
cavity of a chaperonin, translocation through pores, and structure
formation in the exit tunnel of the ribosome. Consequently, free
energies of interaction between amino acid side chains in restricted
spaces can provide insights into factors that control protein stability
in nanopores. Using all-atom molecular dynamics simulations, we show
that 3 pair interactions between side chains - hydrophobic (Ala-Phe),
polar (Ser-Asn) and charged (Lys-Glu) - are substantially altered in
hydrophobic, water-filled nanopores, relative to bulk water. When the
pore holds water at bulk density, the hydrophobic pair is strongly
destabilized and is driven to large separations corresponding to the
width and the length of the cylindrical pore. As the water density is
reduced, the preference of Ala and Phe to be at the boundary decreases,
and the contact pair is preferred. A model that accounts for the volume
accessible to Phe and Ala in the solvent-depleted region near the pore
boundary explains the simulation results. In the pore, the
hydrogen-bonded interactions between Ser and Asn have an enhanced
dependence on their relative orientations, as compared with bulk water.
When the side chains of Lys and Glu are restrained to be side by side,
parallel to each other, then salt bridge formation is promoted in the
nanopore. Based on these results, we argue and demonstrate that for a
generic amphiphilic sequence, cylindrical confinement is likely to
enhance thermodynamic stability relative to the bulk.
Proc. Natl. Acad. Sci. U.
S. A. 2008, 105(46), 17636-17641 |
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Binding
of ADP in the Mitochondrial ADP/ATP Carrier Is Driven by an
Electrostatic Funnel
François
Dehez, Eva Pebay-Peyroula and Christophe Chipot
The ADP/ATP carrier (AAC) is a membrane protein of paramount importance
for the energy-fueling function of the mitochondria, transporting ADP
from the intermembrane space to the matrix and ATP in the opposite
direction. On the basis of the high-resolution, 2.2-Å structure of the
bovine carrier, a total of 0.53 μs of classical molecular dynamics
simulations were conducted in a realistic membrane environment to
decipher the early events of ADP3− translocation across the
inner membrane of the mitochondria. Examination of apo-AAC underscores
the impermeable nature of the carrier, impeding passive transport of
permeants toward the matrix. The electrostatic funnel illuminated from
three-dimensional mapping of the electrostatic potential forms a
privileged passageway anticipated to drive the diphosphate nucleotide
rapidly toward the bottom of the internal cavity. This conjecture is
verified in the light of repeated, independent numerical experiments,
whereby the permeant is dropped near the mouth of the mitochondrial
carrier. Systematic association of ADP3− to the crevice of
the AAC, an early event in its transport across the inner membrane, is
accompanied by the formation of an intricate network of noncovalent
bonds. Simulations relying on the use of an adaptive biasing force
reveal for the first time that the proposed binding site corresponds to
a minimum of the free energy landscape delineating the translocation of
ADP3− in the carrier. The present work paves the way to the
design of novel nucleotides and new experiments aimed at unveiling key
structural features in the chronology of ADP/ATP transport across the
mitochondrial membrane.
J. Am. Chem. Soc. 2008, 130(38), 12725-12733 |
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Free Energy Profile
of H-ras Membrane Anchor upon Membrane Insertion
Alemayehu A. Gorfe, Arneh Babakhani, and J. Andrew McCammon
Angewandte Chemie International Edition
2007, 46(43), 8234-8237 |
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Molecular
Dynamics Study of Small PNA Molecules in Lipid-Water System
Paweł
Weroński , Yi Jiang and Steen Rasmussen
We
present the results of molecular dynamics simulations of small peptide
nucleic acid (PNA) molecules, synthetic analogs of DNA, at a lipid
bilayer in water. At neutral pH, without any salt, and in the
NPn{gamma}T ensemble, two similar PNA molecules (6-mers) with the same
nucleic base sequence and different terminal groups are investigated at
the interface between water and a
1-palmitoyl-2-oleoylphosphatidylcholine lipid bilayer. The results of
our simulations suggest that at low ionic strength of the solution,
both PNA molecules adsorb at the lipid-water interface. In the case
where the PNA molecule has charged terminal groups, the main driving
force of adsorption is the electrostatic attraction between the charged
groups of PNA and the lipid heads. The main driving force of adsorption
of the PNA molecule with neutral terminal groups is the hydrophobic
interaction of the nonpolar groups. Our simulations suggest that the
system free energy change associated with PNA adsorption at the
lipid-water interface is on the order of several tens of kT per PNA
molecule in both cases.
Biophys J. 2007, 92, 3081-3091 |
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Azole-Bridged Diplatinum Anticancer
Compounds. Modulating DNA Flexibility to Escape Repair Mechanism and
Avoid Cross Resistance
Katrin Spiegel, Alessandra Magistrato, Paolo Carloni, Jan Reedijk, and
Michael L. Klein
Dinuclear
azole-bridged Pt compounds bind to DNA helices, forming intrastrand
crosslinks between adjacent guanines in a similar way to cisplatin.
Their cytotoxic profile is, however, different from that of first and
second generation Pt drugs in that they lack cross resistance in
cisplatin-resistant cell lines. In contrast to cisplatin, which induces
a large kink in DNA duplex, structural NMR studies and molecular
dynamics simulations have shown that azole-bridged diplatinum compounds
induce only small structural changes in double-stranded DNA. These
structural differences have been invoked to explain the different
cytotoxic profile of these compounds. Here, we show that in addition to
the small structural changes in DNA, dinuclear Pt compounds also affect
DNA minor groove flexibility in a different way than cisplatin.
Free-energy calculations on azole-bridged diplatinum DNA adducts reveal
that opening of the minor groove requires a higher free-energy cost (G
~ 7-15 kcal/mol) than in the corresponding cisplatin-DNA adduct (G ~ 0
kcal/mol). This could prevent minor groove binding proteins from
binding to diplatinum-DNA adducts thus leading to a different cellular
response than cisplatin and possibly decreasing the activity of
excision repair enzymes. Although the development of drug resistance is
a highly complex mechanism, our findings provide an additional
rationale for the improved cytotoxic activity of these compounds in
cell lines resistant to cisplatin.
J. Phys. Chem. B 2007, 111, 11873-11876 |
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Peptide
hydrolysis in thermolysin: Ab initio QM/MM investigation of the
Glu143-assisted water addition mechanism
Jochen
Blumberger, Guillaume Lamoureux and Michael L. Klein
Thermolysin
(TLN) is one of the best-studied zinc metalloproteases. Yet the
mechanism of action is still under debate. In order to investigate the
energetic feasibility of the currently most favored mechanism, we have
docked a tripeptide to the active site of TLN and computed the free
energy profile at the quantum mechanics/molecular mechanics level of
theory. The mechanism consists of three distinct steps: (i) a Zn-bound
water molecule is deprotonated by Glu143 and attacks the carbonyl bond
of the substrate; (ii) Glu143 transfers the proton to the amide
nitrogen atom; (iii) the nitrogen atom is protonated and the peptide
bond is irreversibly broken. The free energy barriers for steps i and
iii have almost equal heights, 14.8 and 14.7 kcal/mol, respectively,
and are in good agreement with the effective experimental activation
barrier obtained for similar substrates, 12.1-13.6 kcal/mol. Transition
state stabilization for nucleophilic attack is achieved by formation of
a weak coordination bond between the substrate carbonyl oxygen atom and
the Zn ion and of three strong hydrogen bonds between the substrate and
protonated His231 and two solvent molecules. The transition state for
the nucleophilic attack (step i) is more tightly bonded than the
enzyme-substrate complex, implying that TLN complies with Pauling's
hypothesis regarding transition-state stabilization. Glu143, at first
unfavorably oriented for protonation of the amide nitrogen atom,
displayed large structural fluctuations that facilitated reorganization
of the local hydrogen-bond network and transport of the proton to the
leaving group on the nanosecond time scale. The present simulations
give further evidence that Glu143 is a highly effective proton shuttle
which should be assigned a key role in any reaction mechanism proposed
for TLN.
J. Chem. Theor. Comput. 2007,
3, 1837-1850
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Diffusion of
glycerol through
Escherichia
coli aquaglyceroporin GlpF
Jérôme Hénin,
Emad Tajkhorshid, Klaus Schulten and
Christophe Chipot
The
glycerol uptake
facilitator, GlpF, a major
intrinsic
protein found in Escherichia
coli,
conducts selectively water and
glycerol
across the inner membrane. The free energy landscape
characterizing the
assisted transport of glycerol by this homotetrameric
aquaglyceroporin has
been explored by means of equilibrium molecular dynamics over a
time scale
spanning 0.12 μs. In order to overcome the free energy barriers
of the
conduction pathway, an adaptive biasing force (ABF) is applied to the
glycerol
molecule confined in each of the four channels. The results illuminate
the
critical role played by intramolecular relaxation on the diffusion
properties
of the permeant. The present free energy calculations reveal
that glycerol
tumbles and isomerizes on a time scale comparable to that spanned by
its
ABF-assisted conduction in GlpF. As a result, reorientation and
conformational
equilibrium of glycerol in GlpF constitute a bottleneck in the molecular
simulations of the permeation event. A profile characterizing the
position-dependent
diffusion of the permeant has been determined, allowing reaction
rate theory
to be applied for investigating conduction kinetics based on the
measured free
energy landscape.
Biophys.J. 2008, 94, 832-839
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Secondary
and Tertiary Structure Elasticity of
Titin Z1Z2 and a Titin Chain Model
Eric H.
Lee, Jen Hsin, Olga Mayans and Klaus Schulten
The giant
protein titin, which is responsible for passive elasticity
in muscle fibers, is built from 300
regular immunoglobulin-like (Ig) domains and
FN-III
repeats. While the soft elasticity derived from
its
entropic regions, as well as the stiff mechanical resistance
derived
from the unfolding of the secondary structure elements of
Ig- and FN-III domains have been studied extensively, less is
known about the mechanical elasticity stemming from the orientation
of neighboring domains relative to each other.
Here
we address the dynamics and energetics of
interdomain
arrangement of two adjacent Ig-domains of
titin, Z1, and
Z2, using molecular dynamics (MD) simulations.
The
simulations reveal conformational flexibility, due
to the
domain-domain geometry, that lends an intermediate force
elasticity to titin. We employ adaptive biasing force MD
simulations to calculate the energy required to bend the Z1Z2
tandem open to identify energetically feasible interdomain arrangements
of the Z1 and Z2 domains. The finding is cast into a
stochastic model for Z1Z2 interdomain elasticity that is generalized
to a multiple domain chain replicating many
Z1Z2-like
units and representing a long titin segment.
The elastic
properties of this chain suggest that titin
derives
so-called tertiary structure elasticity from
bending and
twisting of its domains. Finally, we employ
steered
molecular dynamics simulations to stretch
individual Z1 and
Z2 domains and characterize the so-called secondary
structure elasticity of the two domains. Our study suggests
that titin's overall elastic response at weak force stems
from a soft entropic spring behavior (not described here), from
tertiary structure elasticity with an elastic spring constant
of
0.001–1 pN/Å and, at strong forces, from secondary
structure
elasticity.
Biophys.J. 2007, 93,
1719-1735
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Energetics of Ion Transport in a
Peptide Nanotube
François Dehez, Mounir Tarek, and Christophe Chipot
Ion channels constitute an important family of integral membrane
proteins responsible for the regulation of ion transport across the
cell membrane. Yet, the underlying energetics of the permeation events
and how the latter are modulated by the environment, specifically near
the mouth of the pore, remain only partially characterized. Here, a
synthetic membrane channel formed by cyclic peptides of alternated D-
and L-hydrophobic -amino acids was considered. The free energy
delineating the translocation of a sodium ion was measured along the
conduction pathway by means of molecular dynamics simulations. The
free-energy profiles that underly the permeation of the open-ended
tubular structure are shown to not only depend on the characteristics
of the latter but also inherently on the location of the mouth of the
synthetic channel with respect to the membrane surface. J. Phys. Chem. B 2007, 111, 10633-10635.
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A
stable water chain in the
hydrophobic
pore of the AmtB
ammonium transporter
Guillaume
Lamoureux, Michael L.
Klein and Simon Bernèche
The
accessibility of water molecules to the
pore of
the AmtB ammonium transporter is studied using molecular dynamics
simulations. Free energy calculations show that the so-called
hydrophobic pore can stabilize a chain of water molecules in a well of
a few kcal/mol, using a favorable electrostatic binding pocket as an
anchoring point. Moreover, the structure of the water chain matches
precisely the electronic density maxima observed in X-ray diffraction
experiments. This result questions the general assumption that the AmtB
pore only contains ammonia (NH3) molecules
diffusing in a
single file fashion. The probable presence of
water
molecules in the pore would influence the relative
stability of NH3 and NH4+,
and thus
calls for a reassessment of the overall permeation mechanism in
ammonium transporters.
Biophys.
J. 2007,
92, L82-L84. |
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Proton
pathways and
H+/Cl- stoichiometry in ClC chloride transporters
Zhifeng
Kuang, Uma Mahankali and Thomas L. Beck
H+/Cl-
antiport behavior has recently been observed in bacterial chloride
channel homologs and eukaryotic CLC-family proteins. The detailed
molecular-level mechanism driving the stoichiometric exchange is
unknown. In the bacterial structure, experiments and modeling studies
have identified two acidic residues, E148 and E203, as key sites along
the proton pathway. The E148 residue is a major component of the fast
gate, and it occupies a site crucial for both H+
and Cl- transport.
E203 is located on the intracellular side of the protein; it is vital
for H+,
but not Cl-, transport. This
suggests two independent ion transit pathways for H+
and Cl- on
the intracellular side of the transporter. Previously, we utilized a
new
pore-searching algorithm, TransPath, to predict Cl-
and H+ ion
pathways in the bacterial ClC channel homolog, focusing on proton
access from the
extracellular solution. Here we employ the TransPath method and
molecular dynamics simulations to explore H+
pathways
linking E148 and E203 in the presence of Cl-
ions
located at the experimentally observed binding sites in the pore. A
conclusion is that
Cl- ions are required at both the intracellular
(Sint) and central
(Scen) binding sites in order
to create an electrostatically favorable H+
pathway
linking E148 and E203; this electrostatic coupling is likely related to
the observed
1H+/2Cl- stoichiometry of
the
antiporter. In addition, we suggest that a tyrosine residue side chain
(Y445), located near the Cl- ion
binding site at Scen, is involved in proton transport between E148 and
E203.
Proteins:
Structure, Function,
and
Bioinformatics 2007, 68,
26-33.
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Barriers to
ion
translocation in cationic and anionic receptors from the Cys-loop family
I. Ivanov,
X. Cheng,
S. M. Sine and J. A. McCammon
Understanding
the
mechanisms of gating and ion permeation in biological channels and
receptors has been a long-standing challenge in biophysics. Recent
advances in structural biology have revealed the architecture of a
number of transmembrane channels and allowed detailed, molecular-level
insight into these systems. Herein, we have examined the barriers to
ion conductance and origins of ion selectivity in models of the
cationic human α7 nicotinic acetylcholine receptor (nAChR)
and the
anionic α1 glycine receptor (GlyR), based on the structure of
Torpedo
nAChR. Molecular dynamics simulations were used to determine water
density profiles along the channel length and established that both
receptor pores were fully hydrated. The very low water density in the
middle of the nAChR pore indicated the existence of a hydrophobic
constriction. By contrast, the pore of GlyR was lined with hydrophilic
residues and remained well hydrated throughout. Adaptive biasing force
simulations allowed us to reconstruct potentials of mean force (PMFs)
for chloride and sodium ions in the two receptors. For the nicotinic
receptor we observed barriers to ion translocation associated with
rings of hydrophobic residues - Val13' and Leu9' - in the middle of the
transmembrane domain. This finding further substantiates the
hydrophobic gating hypothesis for nAChR. The PMF revealed no
significant hydrophobic barrier for chloride translocation in GlyR. For
both receptors non- permeant ions displayed considerable barriers.
Thus, the overall electrostatics and the presence of rings of charged
residues at the entrance and exit of the channels were sufficient to
explain the experimentally observed anion and cation selectivity.
J. Am. Chem. Soc. 2007,
129, 8217-8224.
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Molecular
Dynamics Study of the Inclusion of
Cholesterol into Cyclodextrins
Yanmin Yu, Christophe Chipot, Wensheng Cai, and Xueguang Shao
The interaction of
three cyclodextrins (CDs), viz. β-CD, heptakis
(2,6-di-O-methyl)-β-CD
(DM-β-CD), and 2-hydroxypropyl-β-CD (HP-β-CD), with
cholesterol was investigated using molecular dynamics (MD) simulations.
The free energy along the reaction pathway delineating the inclusion of
cholesterol into each CD was computed using the adaptive biasing force
method. The association constant and the corresponding association free
energy were derived by integrating the potential of mean force (PMF)
over a representative ordering parameter. The results show that the
free energy profiles possess two local minima corresponding to roughly
equally probable binding modes. Among the three CDs, DM-β-CD
exhibits the highest propensity to associate with cholesterol. Ranking
for binding cholesterol, viz. DM-β-CD > HP-β-CD >
β-CD, agrees nicely with experiment. Partitioning of the PMF into
free energy components illuminates that entering of cholesterol into
the CD cavity is driven mainly by electrostatic interactions, whereas
deeper inclusion results from van der Waals forces and solvation
effects. Additional MD simulations were performed to investigate the
structural stability of the host-guest complexes near the free energy
minima. The present results demonstrate that association of cholesterol
and CDs follows two possible binding modes. Although the latter are
thermodynamically favorable for all CDs, one of the two inclusion
complexes appears to be preferred kinetically in the case of
DM-β-CD.
J. Phys. Chem. B 2006 110,
6372-6378.
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Molecular
restraints
in the permeation pathway of ion channels
Werner
Treptow and
Mounir Tarek
Ion
channels assist
and control the diffusion of ions through biological membranes. The
conduction process depends on the structural characteristics of these
nanopores, among which are the hydrophobicity and the afforded diameter
of the conduction pathway. In this contribution, we use full atomistic
free-energy molecular dynamics simulations to estimate the effect of
such characteristics on the energetics of ion conduction through the
activation gate of voltage-gated potassium (Kv) channels. We consider
specifically the ionic translocation through three different permeation
pathways, corresponding to the activation gate of an atomistic model of
Shaker channels in closed and partially opened conformations, and that
of the open conformation of the Kv1.2 channel. In agreement with
experiments, we find that the region of Val478 constitutes the main
gate. The conduction is unfavorable through this gate when the
constriction is smaller than an estimated threshold of
4.5–5.0 Å,
mainly due to incomplete coordination-hydration of the ion. Above this
critical size, e.g., for the Kv1.2, the valine gate is wide enough to
allow fully coordination of the ion and therefore its diffusion on a
flat energy surface. Similar to other ion channels, Kv channels appear
therefore to regulate diffusion by constricting hydrophobic regions of
the permeation pathway.
Biophys.
J. 2006, 91,
L26-L28.
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Reversible
unfolding
of the alanine–rich peptide 3K (Marqusee, S.;
Robbins, V. H.; Baldwin, R. L. Proc. Natl. Acad. Sci. USA 1989, 86,
5286–5290) and its analogue MW (Miick, S.; Martinez, G.;
Fiori, W.;
Todd, A.; Millhauser, G. Nature 1992, 359, 653-655) is examined using
molecular dynamics simulations in explicit water. In both cases,
sampling of the unfolding pathway is obtained on the
ten–nanosecond
time scale by applying an adaptive biasing force. The free energy
profile reveals a single minimum associated with a contiguous a-helix. 310-helical
motifs are observed in folded as well as extended conformations, in
accordance with their proposed role as folding intermediates. The
equilibrium 310-helical
content of both peptides is found, however, to be no higher than a few
percent. Difficulties in both the definition and the detection of
secondary structure motifs, most notably in relation to bifurcated
hydrogen bonds, are proposed to account for the discrepancy between 310-helical
propensities
reported by several authors, based on experimental and computational
results.
J. Phys.
Chem. B 2006, 110, 16718-16723. |
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Insights
into the recognition and association of transmembrane
α-helices. The free energy of α-helix dimerization
in
glycophorin A
Jérôme
Hénin, Andrew Pohorille and Christophe Chipot
The free
energy of
α-helix dimerization of the transmembrane (TM)
region of glycophorin A was estimated from a 125-ns molecular dynamics
(MID) simulation in a membrane mimetic. The free energy profile was
obtained by allowing the TM helical segments to diffuse reversibly
along the reaction pathway. Partition of the potential of mean force
into free energy components illuminates the critical steps of
α-helix recognition and association. At large separations,
the TM
segments are pushed together by the solvent, allowing initial, but not
necessarily native, interhelical interactions to occur. This early
recognition stage precedes the formation of native contacts, which is
accompanied by a tilt of the helices, characteristic of the dimeric
structure. This step is primarily driven by the van der Waals
helix-helix interactions. Free energy perturbation calculations of the
L75A and I76A point mutations reveal a disruption in helix-helix
association due to a loss of favorable dispersion interactions.
Additional MID simulations of the native TM dimer and of a single
α-helix confirm that, prior to association, individual
α-helices are independently stable, in agreement with the
"two-stage" model of integral membrane protein folding.
J.
Am. Chem. Soc. 2005, 127, 8478-8484.
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