Abstract
Substrate transport and diffusion through membrane-bound channels are processes that can span a range of time scales, with only the fastest ones being amenable to most atomic-scale equilibrium molecular dynamics (MD) simulations. However, the application of forces within a simulation can greatly accelerate diffusion processes, revealing important structural and energetic features of the channel. Here, we demonstrate the use of two methods for applying biases to a substrate in a simulation, using the ammonia/ammonium transporter AmtB as an example. The first method, steered MD, applies a constant force or velocity constraint to the substrate, permitting the exploration of potential substrate pathways and the barriers encountered, although typically far outside of equilibrium. On the other hand, the second method, adaptive biasing forces, is quasi-equilibrium, permitting the derivation of a potential of mean force, which characterizes the free energy of the substrate during transport.
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References
Khalili-Araghi F et al (2009) Molecular dynamics simulations of membrane channels and transporters. Curr Opin Struct Biol 19:128–137
Izrailev S et al (1997) Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J 72:1568–1581
Sotomayor M, Schulten K (2007) Single-molecule experiments in vitro and in silico. Science 316:1144–1148
Hummer G, Szabo A (2001) Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc Natl Acad Sci U S A 98:3658–3661
Jarzynski C (1997) Equilibrium free-energy differences from nonequilibrium measurements: a master equation approach. Phys Rev E 56:5018–5035
Jarzynski C (1997) Nonequilibrium equality for free energy differences. Phys Rev Lett 78:2690–2693
Park S et al (2003) Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality. J Chem Phys 119:3559–3566
Park S, Schulten K (2004) Calculating potentials of mean force from steered molecular dynamics simulations. J Chem Phys 120:5946–5961
Darve E, Pohorille A (2001) Calculating free energies using average force. J Chem Phys 115:9169–9183
Darve E, RodrÃguez-Gómez D, Pohorille A (2008) Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys 128:144120
Hénin J, Chipot C (2004) Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys 121:2904–2914
Hénin J et al (2010) Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theor Comp 6:35–47
Chen H et al (2007) Charge delocalization in proton channels. I. The aquaporin channels and proton blockage. Biophys J 92:46–60
Ilan B et al (2004) The mechanism of proton exclusion in aquaporin channels. Proteins 55:223–228
Jensen MØ et al (2002) Energetics of glycerol conduction through aquaglyceroporin. GlpF. Proc Natl Acad Sci U S A 99:6731–6736
Wang Y, Schulten K, Tajkhorshid E (2005) What makes an aquaporin a glycerol channel: a comparative study of AqpZ and GlpF. Structure 13:1107–1118
Wang Y, Tajkhorshid E (2008) Electrostatic funneling of substrate in mitochondrial inner membrane carriers. Proc Natl Acad Sci U S A 105:9598–9603
Celik L, Schiott B, Tajkhorshid E (2008) Substrate binding and formation of an occluded state in the leucine transporter. Biophys J 94:1600–1612
Jensen MØ et al (2007) Sugar transport across lactose permease probed by steered molecular dynamics. Biophys J 93:92–102
Yin Y et al (2006) Sugar binding and protein conformational changes in lactose permease. Biophys J 91:3972–3985
Gumbart J, Wiener MC, Tajkhorshid E (2007) Mechanics of force propagation in TonB-dependent outer membrane transport. Biophys J 93:496–504
Gumbart J, Schulten K (2006) Molecular dynamics studies of the archaeal translocon. Biophys J 90:2356–2367
Gumbart J, Schulten K (2007) Structural determinants of lateral gate opening in the protein translocon. Biochemistry 46:11147–11157
Gumbart J, Schulten K (2008) The roles of pore ring and plug in the SecY protein-conducting channel. J Gen Physiol 132:709–719
Henin J et al (2008) Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys J 94:832–839
Dehez F, Pebay-Peyroula E, Chipot C (2008) Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel. J Am Chem Soc 130:12725–12733
Ivanov I et al (2007) Barriers to ion translocation in cationic and anionic receptors from the cys-loop family. J Am Chem Soc 129:8217–8224
Bostick DL, Brooks CL III (2007) Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel. PLoS Comput Biol 3:e22
Lamoureux G, Klein ML, Bernèche S (2007) A stable water chain in the hydrophobic pore of the AmtB ammonium transporter. Biophys J 92:L82–L84
Lin Y, Cao Z, Mo Y (2006) Molecular dynamics simulations on the Escherichia coli ammonia channel protein AmtB: mechanism of ammonia/ammonium transport. J Am Chem Soc 128:10876–10884
Luzhkov VB et al (2006) Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB. Biochemistry 45:10807–10814
Nygaard TP et al (2006) Ammonium recruitment and ammonia transport by E. coli ammonia channel AmtB. Biophys J 91:4401–4412
Yang H et al (2007) Detailed mechanism for AmtB conducting NH +4 /NH3: molecular dynamics simulations. Biophys J 92:877–885
Khademi S et al (2004) Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 Å. Science 305:1587–1594
Humphrey W, Dalke A, Schulten K (1996) VMD—visual molecular dynamics. J Mol Graph 14:33–38
MacKerell AD Jr et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616
MacKerell AD Jr, Feig M, Brooks CL III (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comp Chem 25:1400–1415
Phillips JC et al (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781–1802
Acknowledgements
This work was supported by the National Institutes of Health (P41-RR005969). Simulations were run at the National Center for Supercomputing Applications (MCA93S028).
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Gumbart, J. (2012). Exploring Substrate Diffusion in Channels Using Biased Molecular Dynamics Simulations. In: Vaidehi, N., Klein-Seetharaman, J. (eds) Membrane Protein Structure and Dynamics. Methods in Molecular Biology, vol 914. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-023-6_19
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DOI: https://doi.org/10.1007/978-1-62703-023-6_19
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