LETTER pubs.acs.org/NanoLett
Generation-Dependent Molecular Recognition Controls Self-Assembly in Supramolecular Dendron-Virus Complexes )
)
Giovanni Doni,†,‡, Mauri A. Kostiainen,§ Andrea Danani,† and Giovanni M. Pavan*,†, †
University of Applied Sciences of Southern Switzerland (SUPSI);Mathematical and Physical Sciences Research Unit (SMF), Centro Galleria 2, Manno, 6928, Switzerland ‡ University of Lugano;Institute of Computational Science, Via Giuseppe Buffi 13, 6906 Lugano, Switzerland § Radboud University Nijmegen;Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
bS Supporting Information ABSTRACT: In this work molecular dynamics simulation identifies a clear link between the dendron-virus multivalent molecular recognition and the nature of the consequent self-assembly. Data demonstrate how a weak hydrophobic association is transformed in an electrostatic self-assembly, orders of magnitude stronger, depending on the dendron generation used to assemble the viruses. This opens a new frontier in the engineering of hierarchical selfassemblies, potentially enabling the control of the supramolecular properties by acting at the single-molecule level. KEYWORDS: Molecular recognition, self-assembly, dendrons, molecular modeling, hierarchical complexes, intermolecular interactions
induced by the first (G1) and second (G2) generation dendrons at low (10 mM) and high (150 mM) NaCl salt concentrations. Parts c and d of Figure 1 show the DLS data for titration of CCMV solution (40 mg L-1) with G1 and G2. In general, G2 was shown to be more effective than G1 in assembling the virus particles, especially when the presence of salt in solution increases (150 mM NaCl). Data showed that, at 10 mM NaCl, the concentration of dendrons needed to assemble 100% of the virus particles is about 1 order of magnitude higher for G1 than for G2 (Figure 1c). The lower efficiency of G1 in driving the selfassembly of virus particles is also more pronounced at 150 mM NaCl;a large excess of G1 is necessary to induce even partial formation of virus assemblies. Graphs in Figure 1c,d10 demonstrate that dendrons are able to assemble the virus particles in a generation-dependent manner, with the larger dendrons (G2) being more efficient. At first sight this generation-dependent salt-sensitivity problem appeared to be similar to the behavior of the same,11 and similar,12 dendron molecules while binding nucleic acids. In order to get a deeper insight in the binding event, initially we studied the molecular recognition of G1 and G2 with the capsid. The CCMV capsid consists of 180 identical coat protein subunits, which adopt an icosahedral assembly (Caspar-Klug
ultivalent interactions1 between synthetic ligands and biological macromolecules have been utilized in diverse biotechnological applications, such as gene delivery vectors,2 sensors3 and advanced materials.4 Dendritic systems are of particular interest as multivalent ligand displays because their branched structure offers a scaffold where functional surface groups can form a well-defined multivalent array.5 Such an array of binding ligands can form high-affinity interactions with biomolecules due to the multivalency effect.6 Multivalent binding of virus particles has been shown for example to prevent human immunodeficiency virus (HIV) infections by blocking the glycoprotein receptors on the virus's surface7 or, on the contrary, to enhance the diffusion-limited transduction of retroviral particles by charge shielding and virus aggregation.8 Cowpea chlorotic mottle virus (CCMV) is an interesting building block for nanotechnology due to its monodisperse structure and ability to reversibly encapsulate materials or scaffold their preparation.9 The possibility to control high-order structures based on protein cage particles (i.e., virus capsids) has significant potential in nanofabrication and fundamental studies of the properties of biohybrid materials with a precise periodic nanoscale architecture. Recently, we reported the possibility to induce self-assembly and optically triggered disassembly of higher-order CCMV particle assemblies using UV-degradable spermine functionalized dendrons (Figure 1a) as molecular “glue” between the virus particles (Figure 1b).10 We employed dynamic light scattering (DLS) to study the assembly of dendron-virus complexes
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r 2010 American Chemical Society
Received: November 2, 2010 Revised: December 1, 2010 Published: December 20, 2010 723
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Figure 1. UV-degradable spermine functionalized dendrons (G1 and G2) are able to induce CCMV virus assembly. (a) Structures of G1 and G2 dendrons used to assemble the virus particles;each spermine surface group (SPM, colored in red) carries nominally a þ3 e charge at neutral pH (total nominal charge: G1, þ9 e; G2, þ27 e; e is the elementary charge). (b) TEM images10 and representative scheme of the CCMV virus assembly induced by the dendrons. DLS data10 for the titrations of CCMV (40 mg L-1) with G1 and G2 in the presence of 10 mM NaCl (c) and 150 mM NaCl (d), volume percentage of the free virus (black symbols, primary axis) and formation of larger secondary assemblies (open green symbols, secondary axis).
triangulation number T = 3) around the viral RNA. The capsid can be further divided into 12 pentamers and 20 hexamers in which the asymmetric unit contains three coat protein units arranged around a pore. Differently from the DNA and RNA double strands, the negative charge density present on the surface of CCMV is lower and not uniformly spread over the capsid surface;in particular, at pH ∼7.4, ∼82% (-540 e) of the total surface charge (-660 e) is prevalently located in the 60 pores (Figure 2), located at the quasi-3-fold axis, in the center of the
asymmetric unit that constitutes the capsid (each pore has a nominal charge of -9 e). We calculated the electrostatic potential in the pore zone (Figure 2b) with the Adaptive PoissonBoltzmann Solver (APBS plugin version 1.1)13 using the PDB2PQR web portal (http://kryptonite.nbcr.net/pdb2pqr/).14,15 Other pores are present in the 5-fold symmetry axes (12 inside the pentamers) and 2-fold symmetry axes (20 inside the hexamers) characterized by an almost neutral charge and were thus not considered in this study.16 724
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Figure 2. (a) Representation of the CCMV capsid virus (structure 1CWP in the Protein Data Bank). Each protein subunit is represented as a “bead”. One of the 60 pores (located at the quasi-3-fold axis, in the middle of the three coat proteins) is represented as black ribbons and highlighted with a red circle. (b) Electrostatic potential surface present at the pore zone. Colors range from 0.0 kT/e (red) to -15.0 kT/e (blue) as shown by the scale bar. (c) The pore region (b) is the base (one side) of the periodic box used for simulations: the pore zone is represented as a purple ribbon, water molecules in cyan. The dendron frame and the SPM ligands are colored in green and red, respectively, ions are omitted for clarity.
Figure 3. G1 and G2 bind with similar affinity but in different manner to the virus surface. (a, b) Side view of the binding site, thermodynamic parameters for the binding event, and scheme of the binding behavior of G1 (a) and G2 (b) dendrons at 10 mM NaCl (see the Supporting Information for the same data in the presence of 150 NaCl). The CCMV surface is represented as gray ribbons. The core (COR), frame and SPM ligands of the dendron are colored in green, yellow, and red, respectively. Water molecules and ions are omitted for clarity. Schemes represent the different binding mode of G1 and G2 that results in a neutral (CCMV-G1) or positively surface charged (CCMV-G2) final complexes.
Figure 2b shows that the negative electrostatic potential decreases rapidly when going outward from the pore, consistent with that seen in previous studies on CCMV virus.16 Each of these negatively charged pores was thus considered as a possible binding site for the positively charged G1 (þ9 e) and G2 (þ27 e) dendrons. We used molecular dynamics simulation to analyze the multivalent molecular recognition between a single dendron (G1 and G2) and the virus surface (Figure 2c) in low (10 mM) and high (150 mM) salt concentrations. As a binding site we chose a portion of the virus surface, which is centered around the pore and large enough to guarantee the correct dynamic behavior of the dendron during the binding (Figure 2b,c). The molecular
dynamics runs were conducted using the AMBER 11 suite of programs.17 The production phase lasted for 10 ns under NPT periodic boundary conditions at 300 K and 1 atm of pressure. The root mean square deviation (rmsd) data were obtained from the molecular dynamics trajectories in order to verify that all of the systems converged to the equilibrium with good stability. The energetic analyses for each system were carried out using the MM-PBSA18 approach according to a validated procedure adopted previously by our group in the study of the molecular recognition between dendritic constructs and nucleic acids (details about the simulations procedure adopted are available in the Supporting Information).11,12,19-22 725
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Figure 4. The different binding modes of G1 and G2 to the virus surface drive two different self-assemblies. (a, b) The virus-virus (V1-V2) interface and the associated thermodynamic parameters generated by G1 (a) and G2 (b) at 10 mM NaCl (pictures and data for the complexes at 150 mM NaCl are available in the Supporting Information). The hydrophobic and electrostatic self-assemblies are illustrated schematically.
Figure 3 reports the thermodynamic data on the binding between dendrons and the CCMV virus at 10 mM NaCl (the same data for the 150 mM systems are available in the Supporting Information). Interestingly both G1 and G2 bind CCMV with similar affinity (the differences in ΔGbind are not statistically relevant) independent of the amount of salt in solution (Supporting Information: ΔGbind is -86.1 ( 6.1 kcal mol-1 and -89.6 ( 6.0 kcal mol-1 for G1 and G2, respectively at 150 mM NaCl). This is due to the different manner of G1 and G2 binding to the capsid surface. G1 is flexible and small enough to adapt to the surface asperity of CCMV and to settle into the pore optimizing the interactions with negatively charged amino acids. On the other hand, only a certain amount of the charge of the bigger G2 can be used productively for the binding; due to a higher rigidity, G2 loses few (Figure 3) SPM units that leave the virus. This is consistent with the binding energetic terms reported by G1 in Figure 3; the enthaplic attraction (ΔHbind) is higher than that for G2, but the same is true for the entropic cost required for the binding process (the fact that G1 is “blocked” over the pore during the binding is also consistent with the dynamic behavior described by the radial distribution function (RDF) plots available in the Supporting Information). Experimental results further support these observations. The ζ-potential of the CCMV-G1 complex is close to neutral (-1.9 mV) while the CCMV-G2 is positively charged (þ23.7 mV).10 Importantly, the molar concentration of G1 per-singlevirus required to fully assemble the virus particles (as calculated from graphs in Figure 1c,d) is largely higher than the one of G2. Surprisingly, ∼324 G1, but only ∼14 G2, molecules per virus are
enough to induce a 100% CCMV assembly at 10 mM NaCl, and these numbers are increased to >5000 G1 and ∼90 G2, respectively, when the NaCl concentration rises to 150 mM (tables with the self-assembly stoichiometry are available in the Supporting Information). Definitely, data show that the binding with CCMV is equally strong for G1 and G2, but the resulting self-assemblies differ by 1-2 orders of magnitude in terms of stability;the different manner with which the two generations bind the virus surface seems indeed to generate two different kinds of self-assemblies. Our view of the phenomenon suggests that G1 saturates the negative surface charge of the CCMV present in the pores; the virus surface is consequently surrounded by G1 that orients the hydrophobic core (COR) toward the external solution. G2, on the other hand, can use the SPM ligands that do not participate actively in the multivalent recognition with CCMV to attract a second virus. This would create two different consequent selfassemblies, characterized by a hydrophobic association (G1) and an electrostatic-driven interaction (G2). To prove the reliability of our hypothesis and to study how the binding of G1 and G2 with virus surface can control the properties of hierarchical assemblies, we created and simulated molecular systems that mimic the interface between two viruses and contain either two G1 dendrons or a single G2 (Figure 4). Due to the different binding modes of G1 and G2, we calculated the energies that drive the self-assembly of the virus particles (ΔGassembly) in different ways. In the virus-virus (V1-V2) interface generated by G1 (Figure 4a), ΔGassembly was calculated as the free energy of binding between the two G1-CCMV complexes. In fact, our 726
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virus surface with equivalent affinity. This is due to the extreme flexibility of the smaller G1, able to fit with the asperities of a protein cage that constitutes the virus and to optimize the interactions. G2 is bigger and more rigid than G1. Moreover, due to its charge excess with respect to the pore (þ27 e vs -9 e) few of its spermine ligands leave the virus and are oriented toward the external solution. As a consequence, the G1-CCMV complex is a neutral and hydrophobic sphere while the G2-CCMV complex is charged and behaves locally as a dipole due to the free spermine ligands of G2. The cohesive energies that drive the formation of hierarchical assemblies differ by more than 1 order on magnitude, demonstrating the different properties of the final virus complexes. The response to the disturbing action by the ions in solution is also different, proving the diverse nature of the interactions that control the virus association. In particular, G1 generates a virus assembly characterized by hydrophobic association, while G2 compacts the capsids electrostatically, with evident consequences on the properties of the final construct. The evidence that the weak interactions generated by each single surface group with the virus surface can act in a concerted manner30 to result in a strong driving force for self-assembly finds consistency also in recent studies on the exceptional mechanical properties of spider silk31 and other biomaterials32 that are controlled by hydrogen bonding interactions. In this perspective, the results of this work highlight the possibility to modulate the properties of the final assembly by acting simply on the dendritic generation, or potentially on other critical easy-to-tune parameters,33 that can control the molecular recognition between dendritic constructs and capsid viruses.
Table 1. The Thermodynamic Energies That Drive the V1-V2 Assembly (ΔGassembly) Generated by the Presence of G1 and G2 in 10 and 150 mM NaCl Solutions (data expressed in kcal mol-1) [NaCl],a mM
10
150
150
G2
G1
G2
ΔGassemblyc
-3.8 ( 0.3 -45.1 ( 3.3 -1.5 ( 0.2 -35.4 ( 2.9
Experimental ionic concentration in solution. b The V1-V2 interface systems generated by the presence of G1 and G2 in solution. c The free energies that drive the V1-V2 assembly are expressed in kcal mol-1 (details on the energetic components are available in the Supporting Information).
energetic analysis demonstrates that each of the two G1 dendrons interacts only with one of the two viruses and is not influenced by the presence of a second one (energetic details in the Supporting Information). The ΔGassembly values generated by G2 were on the other hand obtained as the average of the binding energies between G2 and each of the two viruses (G2-V1 and G2-V2). This was considered to be the most reliable estimation of ΔGassembly due to the complexity of the interface (scheme in Figure 4). The different binding mechanisms of G1 and G2 with the virus surface seem indeed to generate two different kinds of selfassemblies. It is evident that the ΔGassembly values generated by G1 and G2 differ for more than 1 order of magnitude and the difference is further enhanced when the NaCl concentration is increased (Table 1). This is consistent with the graphs reported in Figure 1c,d and explains why, even if G1 and G2 bind with the same efficiency to the virus surface, G2 results in a self-assembly that is evidently more stable than the one induced by G1. It is worth noting that the virus-assembly generated by G1 is most strongly affected by the higher amount of NaCl in solution; ΔGassembly decreases ∼61% when NaCl concentration is increased from 10 to 150 mM. On the other hand, when the virus assembly is driven by G2, ΔGassembly is affected only by ∼21%. Such a difference in response to the same disturbing factor (amount of salt in solution) is clear evidence of the different intermolecular interactions that are involved in the virus assembly in the presence of G1 or G2. Interestingly, the energetics of the virus assembly generated by G1 and G2 are close to the typical values of a hydrophobic association in solution (G1) and an electrostatic intermolecular interaction (G2).23 In fact, saturation of the CCMV pores by G1 neutralizes the virus surface charge and considerably enhances the hydrophobicity of the capsid. As a consequence, the virus particles start to self-assemble to reduce the surface exposed to the solution. In this case, the selfassembly generated by G1 is controlled by a favorable entropy contribution (-TΔSassembly = -3.7 kcal mol-1). Entropy-driven association, accompanied by a lower favorable enthalpy, is typical for hydrophobic association.24-29 On the contrary, the energy that drives the compaction of viruses in the presence of G2 is ∼10-20 times higher and maintains the thermodynamic characteristics of an electrostatic association; ΔGassembly (Figure 4) is largely driven by favorable enthalpy (ΔHassembly = -95.0 kcal mol-1) and opposed by a lower entropy (-TΔSassembly = þ50.0 kcal mol-1). In conclusion, we have reported a molecular dynamics study on the multivalent molecular recognition between sperminefunctionalized dendrons and the CCMV virus. Our exploration of the binding event provided evidence that G1 and G2 bind the
’ ASSOCIATED CONTENT
bS
Supporting Information. Detailed information about the computational methods, the molecular systems simulated in this work, calculated free energies of binding, and RDF plots for the CCMV-dendron complexes at 150 and 10 mM NaCl concentrations. This material is available free of charge via the Internet at http://pubs.acs.org.
’ AUTHOR INFORMATION Corresponding Author
*E-mail:
[email protected]. Author Contributions
)
a
10
V1-V2 assemblyb G1
These authors contributed equally to the work.
’ ACKNOWLEDGMENT The authors acknowledge the COST action TD0802, “Dendrimers in Biomedical Applications”, in favoring this collaborative research program. Professor Rolf Krause, Professor Alessandro De Vita, Professor Jeroen J. L. M. Cornelissen, and Professor Roeland J. M. Nolte are thankfully acknowledged for their fundamental support to the work. G.M.P. was supported by the Swiss State Secretariat for Education and Research (SER). G.D. and A.D. were supported by DECS-Canton Ticino. M.K. was supported by The Netherlands Organization for Scientific Research, Academy of Finland, Instrumentarium Science Foundation, and the Alfred Kordelin Foundation. G.D., A.D., and G.M.P. also acknowledge the CSCS Swiss National Supercomputer Center of Manno (Switzerland) for their technical support 727
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and for the generous access to the 22128 cores of the new Cray XT5-Rosa supercomputer.
(19) Jones, S. P.; Pavan, G. M.; Danani, A.; Pricl, S.; Smith, D. K. Chem.;Eur. J. 2010, 16, 4519–4532. (20) Pavan, G. M.; Danani, A. Phys. Chem. Chem. Phys. 2010, 12, 13914–13917. (21) Pavan, G. M.; Mintzer, M. A.; Simanek, E. E.; Merkel, O. M.; Kissel, T.; Danani, A. Biomacromolecules 2010, 11, 721–730. (22) Pavan, G. M.; Albertazzi, L.; Danani, A. J. Phys. Chem. B 2010, 114, 2667–2675. (23) (a) Anslyn, E. V.; Dougherty, D. A. Modern Physical Organic Chemistry; University Science Books: Sausalito, CA, 2006; pp 145-207. (b) Stone, J. The Theory of Intermolecular Forces; Clarendon Press: Oxford, 1996. (24) Tanford, C. The hydrophobic effect; John Wiley and Sons: New York, 1980. (25) Fenniri, H.; Deng, B.-L.; Ribbe, A. E.; Hallenga, K.; Jacob, J.; Thiyagarajan, P. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6487–6492. (26) Kadler, K. E.; Hojima, Y.; Prockop, D. J. J. Biol. Chem. 1998, 263, 10517–10523. (27) Riedhoff, P.; Schneider, A.; Mandelkow, E.-M.; Mandelkow, E. Biochemistry 1998, 37, 10223–10230. (28) Karr, T. L.; Purich, D. L. Biochem. Biophys. Res. Commun. 1980, 95, 1885–1889. (29) Shalaby, R. A.; Lauffer, M. A. Arch. Biochem. Biophys. 1985, 236, 390–398. (30) Buehler, M. J. Nano Today 2010, 5, 379–383. (31) Keten, S.; Xu, Z.; Ihle, B.; Buehler, M. J. Nat. Mater. 2010, 9, 359–367. (32) Keten, S.; Buehler, M. J. Nano Lett. 2008, 8, 743–748. (33) (a) Tomalia, D. A. Soft Matter 2010, 6, 456–474. (b) Tomalia, D. A. J. Nanopart. Res. 2009, 11, 1251–1310.
’ REFERENCES (1) (a) Badjic, J. D.; Nelson, A.; Cantrill, S. J.; Turnbull, W. B.; Stoddart, J. F. Acc. Chem. Res. 2005, 38, 723–732. (b) Mammen, M.; Choi, S.-K.; Whitesides, G. M. Angew. Chem., Int. Ed. 1998, 37, 2754– 2794. (c) Mulder, A.; Huskens, J.; Reinhoudt, D. N. Org. Biomol. Chem. 2004, 2, 3409–3424. (2) (a) Ferber, D. Science 2001, 294, 1638–1642. (b) GuillotNieckowski, M.; Eisler, S.; Diederich, F. New J. Chem. 2007, 31, 1111–1127. (c) Kukowska-Latallo, J. F.; Bielinska, A. U.; Johnson, J.; Spindler, R.; Tomalia, D. A.; Baker, J. R. Proc. Natl. Acad. Sci. U.S.A. 1996, 93. (3) (a) Bajaj, A.; Miranda, O. R.; Kim, I.-B.; Phillips, R. L.; Jerry, D. J.; Bunz, U. H. F.; Rotello, V. M. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 10912–10916. (b) De, M.; Rana, S.; Akpinar, H.; Miranda, O. R.; Arvizo, R. R.; Bunz, U. H. F.; Rotello, V. M. Nat. Chem. 2009, 1, 461–465. (4) (a) Tong, G. J.; Hsiao, S. C.; Carrico, Z. M.; Francis, M. B. J. Am. Chem. Soc. 2009, 131, 11174–11178. (b) Wesley, W.; Hsiao, S. C.; Carrico, Z. M.; Francis, M. B. Angew. Chem., Int. Ed. 2009, 48, 9493– 9497. (c) Yoo, P. J.; Nam, K. T.; Qi, J.; Lee, S.-K.; Park, J.; Belcher, A. M.; Hammond, P. T. Nat. Mater. 2006, 5, 234–240. (d) Ercolani, G. J. Am. Chem. Soc. 2003, 125, 16097–16103. (e) Mann, S. Nat. Mater. 2009, 8, 781–792. (f) Whitesides, G. M.; Grzybowski, B. Science 2002, 295, 2418–2421. (5) (a) Smith, D. K.; Hirst, A. R.; Love, C. S.; Hardy, J. G.; Brignell, S. V.; Huang, B. Prog. Polym. Sci. 2005, 30, 220–293. (b) Frechet, J. M. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4782–4787. (c) Newkome, G. R.; Shreiner, C. Chem. Rev. 2010, 110, 6338–6442. (6) Lee, C. C.; MacKay, J. A.; Frechet, J. M. J.; Szoka, F. C. Nat. Biotechnol. 2005, 23, 1517–1526. (7) (a) Dezzutti, C. S.; et al. Antimicrob. Agents Chemother. 2004, 48, 3834–3844. (b) Patton, D. L.; Cosgrove Sweeney, Y. T.; McCarthy, T. D.; Hillier, S. L. Antimicrob. Agents Chemother. 2006, 50, 1696–1700. (c) Rupp, R.; Rosenthal, S. L.; Stanberry, L. R. Int. J. Nanomed. 2007, 2, 561–566. (8) Davis, H. E.; Rosinski, M.; Morgan, J. R.; Yarmush, M. L. Biophys. J. 2004, 86, 1234–1242. (9) (a) de la Escosura, A.; Verwegen, M.; Sikkema, F. D.; ComellasAragones, M.; Kirilyuk, A.; Rasing, T.; Nolte, R. J. M.; Cornelissen, J. J. L. M. Chem. Commun. 2008, 44, 1542–1544. (b) Douglas, T.; Young, M. Nature 1998, 393, 152–155. (10) Kostiainen, M. A.; Kasyutich, O.; Cornelissen, J. J.; Nolte, R. J. Nat. Chem. 2010, 2, 394–399. (11) Pavan, G. M.; Kostiainen, M. A.; Danani, A. J. Phys. Chem. B 2010, 114, 5686–5693. (12) Pavan, G. M.; Danani, A.; Pricl, S.; Smith, D. K. J. Am. Chem. Soc. 2009, 131, 9686–9694. (13) Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037–10041. (14) Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A. Nucleic Acids Res. 2007, 35, W522–W525. (15) Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.; Baker, N. A. Nucleic Acids Res. 2004, 32, W665–W667. (16) Zhang, D.; Konecny, R.; Baker, N. A.; McCammon, J. A. Biopolymers 2006, 75, 325–337. (17) Case, D. A.; Darden, T. A.; Cheatham III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Robertson, B..; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Liu, J.; Wu, X.; Brozell, S.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Sangui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 11 In University of California, San Francisco, 2010. (18) Srinivasan, J.; Cheatham, T. E; Cieplak, P.; Kollman, P. A.; Case, D. A. J. Am. Chem. Soc. 1998, 120, 9401–9409. 728
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