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adaptive biasing force
 
Overcoming free energy barriers in molecular simulations using an average force
 


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sugar in membrane

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



Xu 2009

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



CD pmfs

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



cyclodextrins

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



nanopore

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



ATP-ADP transporter

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





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


 


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


 

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


 


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


 




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.


 


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.


 

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.


 

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.