Z-formamidoximes in molecular folding and macrocycles

The formamidoxime configurational Z isomer coupled with the pyridylbiscarboxamide conformational codon were used to fold planar, curved structures. When embedded into macrocycles, this folded motif promotes dimerization through π-π stacking and hydrogen-bonding and the formation of tubules akin to molecular channels in the solid state.     

Helical molecular programming: folding of oligopyridine-dicarboxamides into molecular single helices

Molecular strands composed of alternating 2,6-diaminopyridine and 2,6-pyridinedicarbonyl units have been designed to self-organize into single stranded helical structures upon forming intramolecular hydrogen bonds. Pentameric strands 11, 12, and 14, heptameric strands 1 and 20, and undecameric strand 15 have been synthesized using stepwise convergent strategies. Single helical conformations have been characterized in the solid state by single crystal X-ray diffraction analysis for four of these compounds. Helices from pentameric strands 12 and 14 extend over one turn, and helices from heptameric 20 and undecameric 15 species extend to one and a half and two and a half turns, respectively. Intramolecular hydrogen bonds are responsible for the strong bending of the strands. 1H NMR shifts both in polar and nonpolar organic solvents indicate intramolecular overlap between the peripheral aromatic groups. Thus, helical conformations also predominate in solution. Molecular stochastic dynamic simulations of strand folding starting from a high energy extended linear conformer show a rapid (600 ps at 300 K) conversion into a stable helical conformation.     

The glass transition time scale and configurational entropy in polymers: an experimental molecular view

We report direct experimental observation of local conformational dynamics in a polymer chain at the calorimetric glass transition temperature Tg. Variable-temperature two-dimensional (2D) solid-state exchange NMR, at natural abundance, reveals segmental dynamics in pure polyisobutylene (PIB) occurring on a time scale of several seconds over the Tg range observed by DSC (203-208 K). To our knowledge, this is the first direct observation of molecular-level conformer interchange (trans-trans/trans-gauche/gauche-gauche) at the caloric glass transition temperature. Our results provide a chronologically accurate and pedagogically advantageous demonstration of molecular processes during a polymer phase transition, relative to traditional bulk mechanical and calorimetric techniques. More importantly, we use a miscible blend to demonstrate a general strategy for quantitative evaluation of configurational entropy changes via combination of temperature-dependent 2D exchange NMR and Adams-Gibbs theory. Our results on the Tg time scale are directly relevant to fundamental understanding of the Tg length scale, i.e., the dimension of cooperatively rearranging regions.     

Amine exchange in formamidines: an experimental and theoretical study

N-H-containing formamidines combine a reasonably strong association to carboxylic acids to form complexes of well-defined geometries with a simultaneous proton-induced electrophilicity enhancement that allows for the exchange of their amine portion. The N=C(H)-NH fragment, therefore, undergoes "imine-like" exchange with N-containing nucleophiles. Because of the prototropic equilibrium, the N=C(H)-NH fragment may behave as a "bisimine" centred on the same carbon, in which both N-containing fragments can be exchanged. Considering the proton-induced sensitisation of both C-N units and the well-defined formamidine-carboxylic acid complex geometry, it should be possible to use carboxylic acids as templates for the synthesis of defined architectures by dynamic amine exchange within formamidines. This study highlights three exchange regimes based on the nature of the incoming amine (aliphatic amines, aromatic amines and alkoxyamines), as well as exchange rules based on the amine leaving groups. Following this analysis, a proof of concept for carboxylic acid templated macrocycle formation through dynamic exchange is provided.     

Reversible peptide folding: Dependence on molecular force field used

Temperature‐dependent nuclear magnetic resonance (NMR) and CD spectra of methanol solutions of a β‐heptapeptide have been interpreted in such a way that the secondary structure, a 3₁₄‐helix, is assumed to be stable in a temperature range of between 298 and 393 K. This is in contrast to the results of a 50‐ns molecular dynamics simulation using the GROMOS 96 force field, which found a melting temperature of about 340 K. This discrepancy is addressed by further computational studies using the OPLS‐AA force field. The conformational energetics of N‐formyl‐3‐aminobutanamide in vacuo are obtained using ab initio and density functional quantum‐mechanical calculations at the HF/6‐31G*, B3LYP/6‐31G*, and B3LYP/6‐311+G* levels of theory. The results permit development of torsional parameters for the OPLS‐AA force field that reproduce the conformational energetics of the monomer. By varying the development procedure, three parameter sets are obtained that focus on reproducing either low‐energy or high‐energy conformations. These parameter sets are tested by simulating the reversible folding of the β‐heptapeptide in methanol. The melting temperature of the helix formed (>360 K) is found to be higher than the one obtained from simulations using the GROMOS 96 force field (∼340 K). Differences in the potential energy functions of the latter two force fields are evaluated and point to the origins of the difference in stability. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 774–787, 2000     

Extraction of configurational entropy from molecular simulations via an expansion approximation

A method is presented for extracting the configurational entropy of solute molecules from molecular dynamics simulations, in which the entropy is computed as an expansion of multidimensional mutual information terms, which account for correlated motions among the various internal degrees of freedom of the molecule. The mutual information expansion is demonstrated to be equivalent to estimating the full-dimensional configurational probability density function (PDF) using the generalized Kirkwood superposition approximation (GKSA). While the mutual information expansion is derived to the full dimensionality of the molecule, the current application uses a truncated form of the expansion in which all fourth- and higher-order mutual information terms are neglected. Truncation of the mutual information expansion at the nth order is shown to be equivalent to approximating the full-dimensional PDF using joint PDFs with dimensionality of n or smaller by successive application of the GKSA. The expansion method is used to compute the absolute (classical) configurational entropy in a basis of bond-angle-torsion internal coordinates for several small molecules as well as the change in entropy upon binding for a small host-guest system. Convergence properties of the computed entropy values as a function of simulation time are investigated and comparisons are made with entropy values from the second generation Mining Minima software. These comparisons demonstrate a deviation in -TS of no more than about 2 kcal/mol for all cases in which convergence has been obtained.     

Oscillatory molecular driving force for protein folding at high concentration: a molecular simulation

This paper presents a Langevin dynamics simulation that suggests a novel way to fold protein at high concentration, a fundamental issue in neurodegenerative diseases in vivo and the production of recombinant proteins in vitro. The simulation indicates that the folding of a coarse-grained beta-barrel protein at high concentration follows the "collapse-rearrangement" mechanism but it yields products of various forms, including single proteins in the native, misfolded, and uncollapsed forms and protein aggregates. Misfolded and uncollapased proteins are the "nucleus" of the aggregates that also encapsulate some correctly folded proteins (native proteins). An optimum hydrophobic interaction strength (epsilon*(p)) between the hydrophobic beads of the model protein, which results from a compromise between the kinetics of collapse and rearrangement, is identified for use in increasing the rate of folding over aggregating. Increased protein concentration hinders the structural transitions in both collapse and rearrangement and thus favors aggregation. A new method for protein folding at high concentration is proposed, which uses an oscillatory molecular driving force (epsilon*(p)) to promote the dissociation of aggregates in the low epsilon*(p) regime while promoting folding at a high epsilon*(p). The advantage of this method in enhancing protein folding while depressing aggregation is illustrated by a comparison with the methods based on direct dilution or applying a denaturant gradient.     

Kinetic and thermodynamic control of g-quadruplex folding

A matter of speed: When allowed to fold in a K(+) /poly(ethylene glycol) solution, the guanine?(G)-rich strand of vertebrate telomere DNA forms a parallel/antiparallel G-quadruplex, which is a (3+1) hybrid, within microseconds before slowly transforming into the parallel one within hours. Thus, the conformation that a G-quadruplex initially adopts under physiological conditions may not be the one it adopts at the equilibrium state.     

Accelerated molecular dynamics simulations of protein folding

Folding of four fast‐folding proteins, including chignolin, Trp‐cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred‐of‐microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2–2.1 Å of the native NMR or X‐ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second‐order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein‐folding studies. © 2015 Wiley Periodicals, Inc.     

Protein folding kinetics under force from molecular simulation

Despite a large number of studies on the mechanical unfolding of proteins, there are still relatively few successful attempts to refold proteins in the presence of a stretching force. We explore refolding kinetics under force using simulations of a coarse-grained model of ubiquitin. The effects of force on the folding kinetics can be fitted by a one-dimensional Kramers theory of diffusive barrier crossing, resulting in physically meaningful parameters for the height and location of the folding activation barrier. By comparing parameters obtained from pulling in different directions, we find that the unfolded state plays a dominant role in the refolding kinetics. Our findings explain why refolding becomes very slow at even moderate pulling forces and suggest how it could be practically observed in experiments at higher forces.     

Solid-state molecular folding and supramolecular structures of triptycene-derived secondary dicarboxamides

The synthesis and X-ray crystal structures of triptycene-derived secondary dicarboxamides 1 and 4-7 and reference compounds 2, 3, and 8 are reported. For comparison, molecular conformations of 1-8 in the gas phase and those of 1 and 3-6 in CD2Cl2 investigated by AM1 modeling and 1H NMR spectroscopy, respectively, are also included. The solid-state conformations of 1 and 5-8 are folded and compact, resulting from the cooperative effects of intramolecular amide-amide hydrogen bonding and edge-to-face arene-arene interactions between the triptycene and the N-acetylsulfanilyl groups. The sulfonyl ester groups are also essential in the folding of 1 and 5-8 and function as structural turn units. In contrast, the conformations of 2-4 are unfolded due to the lack of one of these three essentials. The extended triptycene ring systems in 6 and 7 provide an arene-arene contact mode that is different from that for 1 and 5. While AM1 calculations suggest that the two possible arene-arene contact modes in 6 and 7 have similar conformational energies, the one observed in the solid state is also favored in solutions. To achieve a more regular shape for compact crystal packing, the bulky triptycene groups tend to pack in pairs. As a result, the intermolecular amide-amide hydrogen bonding is perturbed and modified with the participation of either the sulfonyl groups or the methanol solvent molecules, leading to various hydrogen-bonding motifs for these triptycene diamides.     

Prospects in computational molecular medicine: a millennial mega-project on peptide folding

During the second half of the 20th century, Molecular Computations have reached to a level that can revolutionize chemistry. The next target will be structural biology, which will be followed soon by Molecular Medicine. The present paper outlines where we are at, in this field, at the end of the 20th century, and in what direction the development may take in the new millennium. In view of the gigantic nature of the problem, it is suggested that a suitably designed cooperative Millennial Mega-project might accelerate our schedule.     

A theoretical study of configurational inversion of 1,1′-binaphthyl by molecular mechanics

The molecular mechanics method has been applied to the study of various pathways and transition states for the configurational inversion of 1,1′-binaphthyl. The preferred pathway is found to be one on the anti (“trans”) side involving one point of H?H nonbonded contact in each of two identical transition states, separated by a very shallow minimum. Very satisfactory agreement with available experimental values for the enthalpy of activation is achieved.     

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations

Using over 75 mus of molecular dynamics simulation, we have generated several thousand folding simulations of the 20-residue Trp cage at experimental temperature and solvent viscosity. A total of 116 independent folding simulations reach RMSDcalpha values below 3 A RMSDcalpha, some as close as 1.4 A RMSDcalpha. We estimate a folding time of 5.5+/-3.5 mus, a rate that is in reasonable agreement with experimental kinetics. Finally, we characterize both the folded and unfolded ensemble under native conditions and note that the average topology of the unfolded ensemble is very similar to the topology of the native state.     

The configurational inversion of methyl-substituted 1,1′-binaphthyls as studied by molecular mechanics

The striking difference in optical stability between 2- and 2.2′-substituted 1.1′-binaphthyls on the one hand, and the corresponding 8- and 8,8′-substituted compounds on the other, has been investigated with the aid of the molecular mechanics method. The calculations suggest reasonable sources of energy differences in both initial and transition states for the pairs of molecules studied, and clearly implicate the peri effect as an important contributor to the increased optical lability of the 8- and 8,8′-substituted compounds.     

Conformational preference and configurational control of highly symmetric spirobi[dibenzazepinium] cation

[formula: see text] Stereodynamics were detected in solution for salts of the simple spirobi[dibenzazepinium] cation in favor of the homochiral (D2) conformer as evidenced by chiral TRISPHAT and BINPHAT counterions; asymmetric induction was furthermore observed in 1H and 15N NMR spectroscopy.     

Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates

Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model should reproduce the thermodynamic and structural properties of the corresponding AL model after mapping to the lower-resolution scale. In the present work, two such models are investigated: (i) the classical GROMOS atomic-level model; (ii) a CG model recently proposed by Marrink et al., which maps approximately four non-hydrogen atoms to one bead [J. Phys. Chem. B 2004, 108, 750]. The study is restricted to n-alkanes whose aliphatic fragments are abundantly found in lipids of biological interest. Additionally, cis-9-octadecene is included, as a template chain of the lipid dioleoylphosphatidylcholine (DOPC). The two representations of molecules in the liquid phase are compared in terms of average molecular structures, extent of configurational space sampled, and single-molecule entropies. An approximate method is used to estimate the rotational contributions to the absolute configurational entropy. Good correspondence between the AL and CG representations is found. The loss in configurational entropy due to the reduction in degrees of freedom upon coarse-graining of the model is estimated.     

Experimental resolution of early steps in protein folding: testing molecular dynamics simulations

Time-resolved Tyr fluorescence spectroscopy coupled with a laser-induced temperature-jump (T-jump) was employed to follow the folding relaxation dynamics of the B-domain of Staphylococcal protein A. The single Tyr is located in helix 1 (H1) and is a sensitive probe of the structure of this helix and the overall helical bundle structure. The results from this study were compared to those from a complementary infrared T-jump study on this protein [Vu, D. M.; Myers, J. K.; Oas, T. G.; Dyer, R. B. Biochemistry 2004, 43, 3582]. Both methods detect a microsecond process that follows the cooperative relaxation of the helical bundle core. However, a fast process (10-7 s) that follows the relaxation of the individual helices was observed only with the infrared probe. Thus, fast formation of H1 is not observed, but rather H1 forms in the microsecond phase, concomitantly with the docking to (and stabilization by) the other two helices to form the helical bundle structure. This observation validates the results of several previous molecular dynamics simulations that predict H1 formation only in the final assembly of the helix bundle.     

Applications of isothermal titration calorimetry in protein folding and molecular recognition

During the past decade, isothermal titration calorimetry (ITC) has developed from a specialist method to a major, commercially available tool in the arsenal directed at understanding molecular interactions. At present, ITC is used to study all types of binding reactions, including protein-protein, protein-ligand, DNA-drug, DNA-protein, receptor-target, and enzyme kinetics, and it is becoming the method of choice for the determination of the thermodynamic parameters associated with the structure transformation of one molecule or non-covalent interaction of two (or more) molecules. Here, the new applications of ITC in protein folding/unfolding and misfolding, as well as its traditional application in molecular interaction/recognition are reviewed, providing an overview of what can be achieved in these fields using this method and what developments are likely to occur in the near future.     

The isomers of 3-methyl pentene-2; configurational assignment and molecular structure by electron diffraction

The two isomers of 3-methyl pentene-2 have been investigated in the vapour phase by electron diffraction. The higher boiling isomer (70.4 °C) has the E-configuration and the isomer boiling at 67.7 °C has the Z-configuration. Bond distances in the E-isomer are: r(CC) = 1.349, r(Csp²-Csp³) = 1.511, r(C-C) = 1.551, r(C-H) = 1.116 Å; in the Z-isomer: r(CC) = 1.344, r(Csp²-Csp³) = 1.508, r(C-C) = 1.553, r(C-H) = 1.114 Å. In both compounds the Csp³-Csp³ bond is at approximately right angles to the plane containing the double bond. The possibility of non-planar arrangements around the double bond is discussed.