Comparison of protein solution structures refined by molecular dynamics simulation in vacuum,with a generalized Born model,and with explicit water

The inclusion of explicit solvent water in molecular dynamics refinement of NMR structures ought to provide the most physically meaningful accounting for the effects of solvent on structure, but is computationally expensive. In order to evaluate the validity of commonly used vacuum refinements and of recently developed continuum solvent model methods, we have used three different methods to refine a set of NMR solution structures of a medium sized protein, Escherichia coliglutaredoxin 2, from starting structures calculated using the program DYANA. The three different refinement protocols used molecular dynamics simulated annealing with the program AMBER in vacuum (VAC), including a generalized Born (GB) solvent model, and a full calculation including explicit solvent water (WAT). The structures obtained using the three methods of refinements were very similar, a reflection of their generally well-determined nature. However, the structures refined with the generalized Born model were more similar to those from explicit water refinement than those refined in vacuum. Significant improvement was seen in the percentage of backbone dihedral angles in the most favored regions of , space and in hydrogen bond pattern for structures refined with the GB and WAT models, compared with the structures refined in vacuum. The explicit water calculation took an average of 200 h of CPU time per structure on an SGI cluster, compared to 15–90 h for the GB calculation (depending on the parameters used) and 2 h for the vacuum calculation. The generalized Born solvent model proved to be an excellent compromise between the vacuum and explicit water refinements, giving results comparable to those of the explicit water calculation. Some improvement for and angle distribution and hydrogen bond pattern can also be achieved by energy minimizing the vacuum structures with the GB model, which takes a much shorter time than MD simulations with the GB model.     

Does water play a structural role in the folding of small nucleic acids?

Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5'-GGGC[GCAA]GCCU-3') via ensemble molecular dynamics simulation and, with nearly 500 micros of aggregate simulation time using an explicit representation of the ionic solvent, report successful ensemble folding simulations with a predicted folding time of 8.8(+/-2.0) micros, in agreement with experimental measurements of approximately 10 micros. Comparing our results to previous folding simulations using the GB/SA continuum solvent model shows that accounting for water-mediated interactions is necessary to accurately characterize the free energy surface and stochastic nature of folding. The formation of the secondary structure appears to be more rapid than the fastest ionic degrees of freedom, and counterions do not participate discretely in observed folding events. We find that hydrophobic collapse follows a predominantly expulsive mechanism in which a diffusion-search of early structural compaction is followed by the final formation of native structure that occurs in tandem with solvent evacuation.     

Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model.

Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent.     

Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models

The treatment of hydration effects in protein dynamics simulations varies in model complexity and spans the range from the computationally intensive microscopic evaluation to simple dielectric screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase. Molecular dynamics (MD) simulations were used to sample potential energy surfaces of the two basins with solvent treated by means of explicit and implicit methods. Implicit solvent methods studied include the generalized Born (GB) model, atomic solvation potential (ASP), and the distance-dependent dieletric constant. By using the linear response approximation (LRA), the explicit solvent calculations determined a free-energy difference that is in excellent agreement with the experimental estimate, while rescoring the protein conformations with GB or the Poisson equation showed inconsistent and inferior results. While the approach of rescoring conformations from explicit water simulations with implicit solvent models is popular among many applications, it perturbs the energy landscape by changing the solvent contribution to microstates without conformational relaxation, thus leading to non-optimal solvation free energies. Calculations applying MD with a GB solvent model produced results of comparable accuracy as observed with LRA, yet the electrostatic free-energy terms were significantly different due to optimization on a potential energy surface favored by an implicit solvent reaction field. The simpler methods of ASP and the distance-dependent scaling of the dielectric constant both produced considerable distortions in the protein internal free-energy terms and are consequently unreliable.     

Free energy landscape of protein folding in water: explicit vs. implicit solvent

The Generalized Born (GB) continuum solvent model is arguably the most widely used implicit solvent model in protein folding and protein structure prediction simulations; however, it still remains an open question on how well the model behaves in these large-scale simulations. The current study uses the beta-hairpin from C-terminus of protein G as an example to explore the folding free energy landscape with various GB models, and the results are compared to the explicit solvent simulations and experiments. All free energy landscapes are obtained from extensive conformation space sampling with a highly parallel replica exchange method. Because solvation model parameters are strongly coupled with force fields, five different force field/solvation model combinations are examined and compared in this study, namely the explicit solvent model: OPLSAA/SPC model, and the implicit solvent models: OPLSAA/SGB (Surface GB), AMBER94/GBSA (GB with Solvent Accessible Surface Area), AMBER96/GBSA, and AMBER99/GBSA. Surprisingly, we find that the free energy landscapes from implicit solvent models are quite different from that of the explicit solvent model. Except for AMBER96/GBSA, all other implicit solvent models find the lowest free energy state not the native state. All implicit solvent models show erroneous salt-bridge effects between charged residues, particularly in OPLSAA/SGB model, where the overly strong salt-bridge effect results in an overweighting of a non-native structure with one hydrophobic residue F52 expelled from the hydrophobic core in order to make better salt bridges. On the other hand, both AMBER94/GBSA and AMBER99/GBSA models turn the beta-hairpin in to an alpha-helix, and the alpha-helical content is much higher than the previously reported alpha-helices in an explicit solvent simulation with AMBER94 (AMBER94/TIP3P). Only AMBER96/GBSA shows a reasonable free energy landscape with the lowest free energy structure the native one despite an erroneous salt-bridge between D47 and K50. Detailed results on free energy contour maps, lowest free energy structures, distribution of native contacts, alpha-helical content during the folding process, NOE comparison with NMR, and temperature dependences are reported and discussed for all five models.     

Protein molecular dynamics with the generalized Born/ACE solvent model

Implicit solvent models are increasingly important for the study of proteins in aqueous solution. Here, the generalized Born (GB) solvent polarization model as implemented in the analytical ACE potential [Schaefer and Karplus (1996) J Phys Chem 100:1578] is used to perform molecular dynamics simulations of two small, homologous proteins: the immunoglobulin-binding domain of streptococcal protein G and the Ras binding domain of Raf. Several model parameterizations are compared through more than 60 ns of simulation. Results are compared with two simpler solvent models-an accessible surface area model and a distant-dependent dielectric model, with finite-difference Poisson calculations, with existing explicit solvent simulations, and with experimental data. The simpler models yield stable but distorted structures. The best GB/ACE implementation uses a set of atomic Voronoi volumes reported recently, obtained by averaging over a large database of crystallographic protein structures. A 20% reduction is applied to the volumes, compensating in an average sense for an excessive de-screening of individual charges inherent in the ACE self-energy and for an undersolvation of dipolar groups inherent in the GB screening function. This GB/ACE parameterization yields stable trajectories on the 0.5-1-ns time scale that deviate moderately (approximately 1.5-2.5 A) from the X-ray structure, reproduce approximately the surface distribution of charged, polar, and hydrophobic groups, and reproduce accurately backbone flexibility as measured by amide NMR-order parameters. Over longer time scales (1.5-3 ns), some of the protein G runs escape from the native energy basin and deviate strongly (3 A) from the native structure. The conformations sampled during the transition out of the native energy basin are overstabilized by the GB/ACE solvation model, as compared with a numerical treatment of the full dielectric continuum model.     

Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88

Elucidating the relationship between sequence and conformation is essential for the understanding of functions of proteins. While sharing 88 % sequence identity and differing by only seven residues, GA88 and GB88 have completely different structures and serve as ideal systems for investigating the relationship between sequence and function. Benefiting from the continuous advancement of the computational ability of modern computers, molecular dynamics (MD) simulation is now playing an increasingly important role in the study of proteins. However, the reliability of MD simulations is limited by the accuracy of the force fields and solvent model approximations. In this work, several AMBER force fields (AMBER03, AMBER99SB, AMBER12SB, AMBER14SB, AMBER96) and solvent models (TIP3P, IGB5, IGB7, IGB8) have been employed in the simulations of GA88 and GB88. The statistical results from 19 simulations show that GA88 and GB88 both adopt more compact structures than the native structures. GB88 is more stable than GA88 regardless of the force fields and solvent models utilized. Most of the simulations overestimated the salt bridge interaction. The combination of AMBER14SB force field and IGB8 solvent model shows the best overall performance in the simulations of both GA88 and GB88. AMBER03 and AMBER12SB also yield reasonable results but only in the TIP3P explicit solvent model.     

Comparison of (13)C(alpha)H and (15)NH backbone dynamics in protein GB1

This study presents a site-resolved experimental view of backbone C(alpha)H and NH internal motions in the 56-residue immunoglobulin-binding domain of streptococcal protein G, GB1. Using (13)C(alpha)H and (15)NH NMR relaxation data [T(1), T(2), and NOE] acquired at three resonance frequencies ((1)H frequencies of 500, 600, and 800 MHz), spectral density functions were calculated as F(omega) = 2omegaJ(omega) to provide a model-independent way to visualize and analyze internal motional correlation time distributions for backbone groups in GB1. Line broadening in F(omega) curves indicates the presence of nanosecond time scale internal motions (0.8 to 5 nsec) for all C(alpha)H and NH groups. Deconvolution of F(omega) curves effectively separates overall tumbling and internal motional correlation time distributions to yield more accurate order parameters than determined by using standard model free approaches. Compared to NH groups, C(alpha)H internal motions are more broadly distributed on the nanosecond time scale, and larger C(alpha)H order parameters are related to correlated bond rotations for C(alpha)H fluctuations. Motional parameters for NH groups are more structurally correlated, with NH order parameters, for example, being larger for residues in more structured regions of beta-sheet and helix and generally smaller for residues in the loop and turns. This is most likely related to the observation that NH order parameters are correlated to hydrogen bonding. This study contributes to the general understanding of protein dynamics and exemplifies an alternative and easier way to analyze NMR relaxation data.     

Acceptable protein and solvent behavior in primary hydration shell simulations of hen lysozyme

The "primary hydration shell" method in molecular dynamics simulations uses a two- to three-layer thick shell of explicitly represented water molecules as the solvent around the protein of interest. We show that despite its simplicity, this computationally cheap model is capable of predicting acceptable water and protein behavior using the CHARMM22/CMAP potential function. For protein dynamics, comparisons are made with Lipari-Szabo order parameters. These have been derived from NMR relaxation parameters for pico-nano second motions of the NH groups in the main-chain and NH(2) groups in Asn/Gln side chains in hen lysozyme. It is also shown that an even simpler, and therefore faster, water-shell model leads to results in similarly good agreement with experiments, and also compared with simulations using a full box of water with periodic boundary conditions or with an implicit solvation model. Thus, the primary hydration shell method should be useful in making larger systems accessible to extensive simulations.     

The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease

The hydrogen-bond network in various stages of the enzymatic reaction catalyzed by HIV-1 protease was studied through quantum-classical molecular dynamics simulations. The approximate valence bond method was applied to the active site atoms participating directly in the rearrangement of chemical bonds. The rest of the protein with explicit solvent was treated with a classical molecular mechanics model. Two possible mechanisms were studied, general-acid/general-base (GA/GB) with Asp 25 protonated at the inner oxygen, and a direct nucleophilic attack by Asp 25. Strong hydrogen bonds leading to spontaneous proton transfers were observed in both reaction paths. A single-well hydrogen bond was formed between the peptide nitrogen and outer oxygen of Asp 125. The proton was diffusely distributed with an average central position and transferred back and forth on a picosecond scale. In both mechanisms, this interaction helped change the peptide-bond hybridization, increased the partial charge on peptidyl carbon, and in the GA/GB mechanism, helped deprotonate the water molecule. The inner oxygens of the aspartic dyad formed a low-barrier, but asymmetric hydrogen bond; the proton was not positioned midway and made a slightly elongated covalent bond, transferring from one to the other aspartate. In the GA/GB mechanism both aspartates may help deprotonate the water molecule. We observed the breakage of the peptide bond and found that the protonation of the peptidyl amine group was essential for the peptide-bond cleavage. In studies of the direct nucleophilic mechanism, the peptide carbon of the substrate and oxygen of Asp 25 approached as close as 2.3 A.     

Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation.

The dielectrically consistent reference interaction site model (DRISM) integral equation theory is applied to determine the potential of mean force (PMF) for an alanine tetramer. A stochastic dynamics simulation of the alanine tetramer using this PMF is then compared with an explicit water molecular dynamics simulation. In addition, comparison is also done with simulations using other solvent models like the extended reference interaction site model (XRISM) theory, constant dielectric and linear distance-dependent dielectric models. The results show that the DRISM method offers a fairly accurate and computationally inexpensive alternative to explicit water simulations for studies on small peptides.     

Parameterization and Application of an Implicit Solvent Model for Macromolecules

Abstract

As the field of theoretical biophysics begins to recognize systems of longer timescales and larger magnitude, rapid approaches for investigating these systems are required. One promising simplification of the typical system of a solute surrounded by water is the use of implicit solvation models. The generalized Born implicit solvent offers a rapid approach for computing the electrostatic effects of bulk solvent without the explicit representation of water molecules. This report describes the parameterization of a generalized Born (GB) model for protein and nucleic acid structures. As a demonstration of the usefulness of this approach, the GB model is applied toward the discrimination of misfolded and properly folded protein structures. This study attempts to illustrate the potential of the GB model for molecular dynamics simulations over longer timescales as well as for screening large structural databases.     

A Novel Implicit Solvent Model for Simulating the Molecular Dynamics of?RNA

Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin–Debye model and the Poisson–Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.     

Conformation in solution and dynamics of a structurally constrained linear insect kinin pentapeptide analogue

The preferred conformations of the active diuretic insect kinin pentapeptide analogue Phe-Phe-Aib-Trp-Gly-NH2 were studied using nmr spectroscopy and molecular modeling. Structure sets consistent with rotating frame nuclear Overhauser effect spectroscopy distance constraints obtained by restrained simulated annealing in vacuo indicate a predominant population of a type II beta-turn involving the Phe1-Trp4 region. An equilibrium between this type II and a type I beta-turn formed by residues Phe2 and Gly5 was observed in a 5 ns restrained molecular dynamics simulation using the implicit generalized Born solvent accessible surface area (GB/SA) solvation model. When subjected to 500 ps dynamics with explicit water both beta-turn folds were conserved throughout the simulations. The results obtained with implicit and explicit solvation models are compared, and their consistency with the nmr observations is discussed. The behavior of the linear pentapeptide in this study is in agreement with an earlier report on the consensus conformation of the insect kinin active core derived from analysis of cyclic active analogues.     

A Novel Implicit Solvent Model for Simulating the Molecular Dynamics of RNA

Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin–Debye model and the Poisson–Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.     

Folding thermodynamics of β‐hairpins studied by replica‐exchange molecular dynamics simulations

We study the differences in folding stability of β‐hairpin peptides, including GB1 hairpin and a point mutant GB1 K10G, as well as tryptophan zippers (TrpZips): TrpZip1, TrpZip2, TrpZip3‐1, and TrpZip4. By performing replica‐exchange molecular dynamics simulations with Amber03* force field (a modified version of Amber ff03) in explicit solvent, we observe ab initio folding of all the peptides except TrpZip3‐1, which is experimentally known to be the least stable among the peptides studied here. By calculating the free energies of unfolding of the peptides at room temperature and folding midpoint temperatures for thermal unfolding of peptides, we find that TrpZip4 and GB1 K10G peptides are the most stable β‐hairpins followed by TrpZip1, GB1, and TrpZip2 in the given order. Hence, the proposed K10G mutation of GB1 peptide results in enhanced stability compared to wild‐type GB1. An important goal of our study is to test whether simulations with Amber 03* model can reproduce experimentally predicted folding stability differences between these peptides. While the stabilities of GB1 and TrpZip1 yield close agreement with experiment, TrpZip2 is found to be less stable than predicted by experiment. However, as heterogenous folding of TrpZip2 may yield divergent thermodynamic parameters by different spectroscopic methods, mismatching of results with previous experimental values are not conclusive of model shortcomings. For most of the cases, molecular simulations with Amber03* can successfully reproduce experimentally known differences between the mutated peptides, further highlighting the predictive capabilities of current state‐of‐the‐art all‐atom protein force fields. Proteins 2015; 83:1307–1315. © 2015 Wiley Periodicals, Inc.     

Conformational sampling with implicit solvent models: application to the PHF6 peptide in tau protein

Implicit solvent models approximate the effects of solvent through a potential of mean force and therefore make solvated simulations computationally efficient. Yet despite their computational efficiency, the inherent approximations made by implicit solvent models can sometimes lead to inaccurate results. To test the accuracy of a number of popular implicit solvent models, we determined whether implicit solvent simulations can reproduce the set of potential energy minima obtained from explicit solvent simulations. For these studies, we focus on a six-residue amino-acid sequence, referred to as the paired helical filament 6 (PHF6), which may play an important role in the formation of intracellular aggregates in patients with Alzheimer's disease. Several implicit solvent models form the basis of this work--two based on the generalized Born formalism, and one based on a Gaussian solvent-exclusion model. All three implicit solvent models generate minima that are in good agreement with minima obtained from simulations with explicit solvent. Moreover, free-energy profiles generated with each implicit solvent model agree with free-energy profiles obtained with explicit solvent. For the Gaussian solvent-exclusion model, we demonstrate that a straightforward ranking of the relative stability of each minimum suggests that the most stable structure is extended, a result in excellent agreement with the free-energy profiles. Overall, our data demonstrate that for some peptides like PHF6, implicit solvent can accurately reproduce the set of local energy minimum arising from quenched dynamics simulations with explicit solvent. More importantly, all solvent models predict that PHF6 forms extended beta-structures in solution, a finding consistent with the notion that PHF6 initiates neurofibrillary tangle formation in patients with Alzheimer's disease.     

A comparison of DMPC- and DLPE-based lipid bilayers.

A 250 ps molecular dynamics simulation of the dimyristoylphosphatidylcholine (DMPC)-based lipid bilayer, including explicit water molecules, is reported. The solvent environment of the head groups and other structural properties of the bilayer have been analyzed and compared with experimental results as well as our previous simulation of the dilauroylphosphatidylethanolamine (DLPE)-based bilayer. From this comparison we find that the solvent structure around the DMPC head group (clathrate shell) is significantly different than that around the DLPE head group (typical hydrogen bonding interactions). We have modeled the probable relationship between the different solvent environments around the R-N(CH3)3+ (DMPC) and R-NH3+ (DLPE) head groups and the different interlammelar distances in these systems by performing potential of mean force (PMF) simulations on two N(CH3)4+ and NH4+ ions in water. From the PMF simulations it appears that the differences in the hydration of the DMPC and DLPE head groups is not responsible for the differences in the hydration force observed for these systems. We also find that the orientational polarization of DLPE and DMPC is similar, which suggests that solvent polarization is not responsible for the differences in the hydration repulsion behavior observed in these systems. We also examined the order parameters for DMPC and found them to be in reasonable agreement with experiment. Given the different characteristics of the DLPE and DMPC head groups, we suggest an explanation of the differences in the interlammellar spacings of bilayers composed of these like-charged lipids. From our DLPE simulations we find that the R-NH3+ head groups can interact with the nonesterified oxygens of the phosphate group in an intraleaflet or an interleaflet manner. For the latter a "cross link" between two leaflets can be formed, which causes a stabilization of the interlamellar spacings at fairly short distances. Moreover, due to the strong intraleaflet interaction we find that the DLPE interface is relatively "flat" (as opposed to DMPC-based bilayers), which results in a surface that has regions of positive and negative charge that reside in the same plane along the bilayer normal. Based on this we propose that the DLPE bilayer interface can correlate itself with another DLPE interface by alignment of the regions of positive (or negative) charge on one leaflet with the opposite charges on the opposing leaflet.     

An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme

In this report we examine several solvent models for use in molecular dynamics simulations of protein molecules with the Discover program from Biosym Technologies. Our goal was to find a solvent system which strikes a reasonable balance among theoretical rigor, computational efficiency, and experimental reality. We chose phage T4 lysozyme as our model protein and analyzed 14 simulations using different solvent models. We tested both implicit and explicit solvent models using either a linear distance-dependent dielectric or a constant dielectric. Use of a linear distance-dependent dielectric with implicit solvent significantly diminished atomic fluctuations in the protein and kept the protein close to the starting crystal structure. In systems using a constant dielectric and explicit solvent, atomic fluctuations were much greater and the protein was able to sample a larger portion of conformational space. A series of nonbonded cutoff distances (9.0, 11.5, 15.0, 20.0 Å) using both abrupt and smooth truncation of the nonbonded cutoff distances were tested. The method of dual cutoffs was also tested. We found that a minimum nonbonded cutoff distance of 15.0 Å was needed in order to properly couple solvent and solute. Distances shorter than 15.0 Å resulted in a significant temperature gradient between the solvent and solute. In all trajectories using the proprietary Discover switching function, we found significant denaturation in the protein backbone; we were able to run successful trajectories only in those simulations that used no switching function. We were able to significantly reduce the computational burden by using dual cutoffs and still calculate a quality trajectory. In this method, we found that an outer cutoff distance of 15.0 Å and an inner cutoff distance of 11.5 worked well. While a 10 Å shell of explicit water yielded the best results, a 6 A shell of water yielded satisfactory results with nearly a 40% reduction in computational cost. © 1994 John Wiley & Sons, Inc.     

Conformational effects of C(alpha,alpha)-dipropargylglycine as a constrained residue

A useful synthon to approach artificial phenylalanyl peptides in a [2 + 2 + 2] cycloaddition reaction, C(alpha,alpha)-dipropargylglycine (Dprg) is examined for its conformational preferences as a constrained residue. Crystal structure analysis and preliminary NMR results establish possible preference of the residue for folded (alpha) rather than extended (beta) region of the straight phi,psi conformational space. Boc-Dprg-L-Leu-OMe (1) displays two molecular conformations within the same crystallographic asymmetric unit, with Dprg in the alpha(R) or alpha(L) conformation, participating in a type I beta-turn or an alpha(L)-alpha(R)-type fold, in which Leu(2) assumes the alpha(R) conformation stereochemically favored for an L-chiral residue. Boc-Dprg-D-Val-L-Leu-OMe (2) displays a type I' beta-turn conformation in crystal, with both Dprg(1) and D-Val(2) assuming the alpha(L) conformation stereochemically favored for a D-chiral residue, with 4 --> 1 type hydrogen bond linking L-Leu(3) NH with Boc CO. NMR analysis using temperature variation, solvent titration, and a spin probe study suggests a fully solvent-exposed nature of Dprg NH, ruling out a fully extended C(5)-type conformation for this residue, and solvent sequestered nature of L-Leu(3) NH, suggesting possibility of a beta-turn due to Dprg assuming a folded conformation.