Monte Carlo simulations of conformations of chain molecules in a cylindrical pore

Off-lattice Monte Carlo simulations are employed to study the behavior of chain molecules confined in a long cylindrical pore under the condition of hard-body interaction. The emphasis is placed on the chain and bead distributions as well as the location dependence of the chain conformation and anisotropy. The simulation results show that the chains very near the pore surface tend to wrap around the surface in various configurations. This behavior is qualitatively similar to that of the chains near but outside a cylindrical rod. Moreover, the bead concentration near the pore surface increases with increasing surface curvature.     

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

A new adaptive umbrella sampling technique for molecular dynamics simulations is described. The high efficiency of the technique renders multidimensional adaptive umbrella sampling possible and thereby enables uniform sampling of the conformational space spanned by several degrees of freedom. The efficiency is achieved by using the weighted histogram analysis method to combine the results from different simulations, by a suitable extrapolation scheme to define the umbrella potential for regions that have not been sampled, and by a criterion to identify simulations during which the system was not in equilibrium. The technique is applied to two test systems, the alanine dipeptide and the threonine dipeptide, to sample the configurational space spanned by one or two dihedral angles. The umbrella potentials applied at the end of each adaptive umbrella sampling run are equal to the negative of the corresponding potentials of mean force. The trajectories obtained in the simulations can be used to calculate dynamical variables that are of interest. An example is the distribution of the distance between the HN and the Hβ proton that can be important for the interpretation of NMR experiments. Factors influencing the accuracy of the calculated quantities are discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1450–1462, 1997     

Quantitative prediction of amyloid fibril growth of short peptides from simulations: calculating association constants to dissect side chain importance

Quantitative prediction of the fibril growth properties of different peptides is conducted with a molecular dynamics approach. Association constants of small peptides used as a model for amyloid formation are calculated, and the results show very good agreement with experiments. Also the free-energy differences associated with two important interactions that characterize fibril growth, namely cross-beta-sheet and lateral interactions, are obtained. These two interactions show different dependencies on the physicochemical properties of the side chains, explaining the variation in fibril morphologies between different peptides.     

Molecular dynamics simulations of side chain liquid crystal polymer molecules in isotropic and liquid-crystalline melts

A detailed molecular dynamics simulation study is described for a polysiloxane side chain liquid crystal polymer (SCLCP). The simulations use a coarse-grained model composed of a combination of isotropic and anisotropic interaction sites. On cooling from a fully isotropic polymer melt, we see spontaneous microphase separation into polymer-rich and mesogen-rich regions. Upon application of a small aligning potential during cooling, the structures that form on microphase separation anneal to produce a smectic-A phase in which the polymer backbone is largely confined between the smectic layers. Several independent quenches from the melt are described that vary in the strength of the aligning potential and the degree of cooling. In each quench, defects were found where the backbone chains hop from one backbone-rich region to the next by tunneling through the mesogenic layers. As expected, the number of such defects is found to depend strongly on the rate of cooling. In the vicinity of such a defect, the smectic-A structure of the mesogen-rich layers is disrupted to give nematiclike ordering. Additionally, several extensive annealing runs of approximately 40 ns duration have been carried out at the point of microphase separation. During annealing the polymer backbone is seen to be slowly excluded from the mesogenic layers and lie perpendicular to the smectic-A director. These observations agree with previous assumptions about the structure of a SCLCP and with interpretations of x-ray diffraction and small angle neutron scattering data. The flexible alkyl spacers, which link the backbone to the mesogens, are found to form sublayers around the backbone layer.     

Solution conformations of the immunomodulator muramyl peptides

MDP, Murabutide and the MDP[D-Ala) analogue have been studied dissolved in dimethylsulfoxyde by means of ¹H-n.m.r., including the 2D.2Q ¹H-¹H inadequate and NOESY (Nuclear Overhauser Effect Spectroscopy) experiments. The results confirm the “S” shaped conformation constituted by two adjacent β turns in MDP. The first turn is a tight “type II β turn” and takes place around the MurNac (N-acetylmuramic acid) moiety of MDP and Murabutide and is stabilized by a C₁₀ hydrogen bonding between the Ala NH (1 + 3) and the acetamido C = 0 (1). The second turn is centered around L-Ala-D-iGln and requires the α-carboxamide group of D-iGln for its stabilization and thus does not occur in Murabutide. The L-Ala → D-Ala Inversion in MDP[D-Ala] produces substantial conformational modifications leading to a cyclic structure with the iGln α-carboxamide protons and the acetamido methyl group in close spatial proximity. The dissociation of the adjuvant, antiinfection and pyrogenic activities in the 3 compounds is well depicted by these variations of conformations.     

Folding thermodynamics of pseudoknotted chain conformations

We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains. For the mechanical unfolding process, we predict the force-extension curves, from which we can obtain the information about structural transitions in the unfolding process. In general, a pseudoknotted structure unfolds through multiple structural transitions. The interplay between the helix stems and the loops plays an important role in the folding stability of pseudoknots. For instance, variations in loop sizes can lead to the destabilization of some intermediate states and change the (equilibrium) folding pathways (e.g., two helix stems unfold either cooperatively or sequentially). In both thermal and mechanical unfolding, depending on the nucleotide sequence, misfolded intermediate states can emerge in the folding process. In addition, thermal and mechanical unfoldings often have different (equilibrium) pathways. For example, for certain sequences, the misfolded intermediates, which generally have longer tails, can fold, unfold, and refold again in the pulling process, which means that these intermediates can switch between two different average end-end extensions.     

Stable helical peptoids via covalent side chain to side chain cyclization

Peptoids are oligomeric N-substituted glycines with potential as biologically relevant compounds. Helical peptoids provide an attractive fold for the generation of protein-protein interaction inhibitors. The generation of helical peptoid folds in organic and aqueous media has been limited to strict design rules, as peptoid-folding is mainly directed via the steric direction of alpha-chiral side-chains. Here a new methodology is presented to induce helical folds in peptoids with the aid of side chain to side chain cyclization. Cyclic peptoids were generated via solid-phase synthesis and their folding was studied. The cyclization induces significant helicity in peptoids in organic media, aids the folding in aqueous media, and requires the incorporation of only relatively few chiral aromatic side chains.     

Monte Carlo simulations for the study of hemoglobin-fragment conformations

Monte Carlo simulations have been performed to study the conformations of the pentapeptide fragments of normal adult (Thr-Pro-Glu-Glu-Lys) and sickle-like anemia hemoglobin (Thr-Pro-Val-Glu-Lys). The results show that the energy optimized conformation of normal adult hemoglobin-fragment agrees with the X-ray experiment and the theoretically determined conformation of the sickle-like anemia hemoglobin-fragment is identical with the conformation of the normal adult hemoglobin-fragment.     

Accessing the disallowed conformations of peptides employing amide-to-imidate modification

Selective modification of the C-terminal amide in peptides to dihydrooxazine (a novel stable imidate isostere) by intramolecular nucleophilic cyclo-O-alkylation of the corresponding N-(3-bromopropyl)amides results in constraining of the C-terminal residue in natively disallowed conformations both in crystals and in solution.     

Hamiltonian replica‐exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles

A Hamiltonian Replica‐Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two‐dimensional backbone and one‐dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions. © 2013 Wiley Periodicals, Inc.     

Coexistence of two different side chain packing structures in a smectic phase of liquid-crystalline side chain polymers

Ten varieties of liquid-crystalline side chain polymers, poly(cholesteryl-ω-(methacryloyloxy)alkanoates) (pChMO-n, n = 1, 2, 3, 4, 5, 7, 9, 10, 11 and 15; the carbon number of the alkyl chain), were studied by differential scanning calorimetry and small angle X-ray scattering. On and after the first cooling run from the isotropic state, these polymethacrylates gave the same smectic phase. X-ray investigations showed that pChMO-n with short spacers (n = 1-7) has a two layer (bilayer) S_A packing structure, and pChMO-n with a longer spacer (n= 15) has a single layer (monolayer) S_A packing structure. However, these two types of packing structure appear simultaneously in pChMO-n (n = 9s-11) below their phase transition temperature. To clarify the manner of the coexistence of the two different structures the smectic layer spacing and X-ray diffraction patterns were examined by small angle X-ray scattering at various temperatures.     

Analysis of the RGD sequence in protein structures: comparison to the conformations of the RGDW and DRGDW peptides determined by molecular dynamics simulations

Geometric properties of the RGD sequence in a data set of protein crystal and NMR structures deposited in the Protein Data Bank were examined to identify structural characteristics that are related to cell adhesion activity. Interatomic distances and dihedral angles are examined. These geometric measures are then used in an analysis of the conformations of the RGDW and _DRGDW peptides obtained from molecular dynamics simulations (Stote RH, et al. (2000) J Phys ChemB 104:1624). This analysis leads to the suggestion that differences in the accessible conformations contribute to the difference in biological activity between the RGDW and the _DRGDW peptides. Received: 15 August 2000 / Accepted: 4 October 2000 / Published online: 21 March 2001     

Mechanisms for the selective gas-phase fragmentation reactions of methionine side chain fixed charge sulfonium ion containing peptides

To enable the development of improved tandem mass spectrometry based methods for selective proteome analysis, the mechanisms, product ion structures, and other factors influencing the gas-phase fragmentation reactions of methionine side-chain derivatized "fixed-charge" phenacylsulfonium ion containing peptide ions have been examined. Dissociation of these peptide ions results in the exclusive characteristic loss of the derivatized side chain, thereby enabling their selective identification. The resultant product ion(s) are then subjected to further dissociation to obtain sequence information for subsequent protein identification. Molecular orbital calculations (at the B3LYP/6-31 + G (d,p) level of theory) performed on a simple peptide model, together with experimental evidence obtained by multistage dissociation of a regioselectively deuterated methionine derivatized sulfonium ion containing tryptic peptide, indicate that fragmentation of the fixed charge containing peptide ions occurs via SN2 reactions involving the N- and C-terminal amide bonds adjacent to the methionine side chain, resulting in the formation of stable cyclic five- and six-membered iminohydrofuran and oxazine product ions, respectively. These studies further indicate that the rings formed via these neighboring group reactions are stable to further dissociation by MS3. As a consequence, the formation of b- or y-type sequence ions are "skipped" at the site of cyclization. Despite this, complete sequence information is still obtained because of the presence of both cyclic products.     

Comparative study of global minimum energy conformations of hydrated peptides

A global optimization method is described for identifying the global minimum energy conformation, as well as lower and upper bounds on the global minimum conformer of solvated peptides. In considering the effects of hydration, two independent continuum-based solvation models are employed. The first method is based on the calculation of solvent-accessible surface areas, whereas the second method uses information on the solvent-accessible volume of hydration shells. The hydration effects predicted by the area- and volume-based models, using a variety of atomic solvation parameter (ASP) sets, are tested and compared by identifying global minimum energy structures of terminally blocked peptides and oligopeptides. Significant differences are observed, indicating that appropriate model selection is essential for accurately predicting hydrated peptide structures. Using this information, the applicability of these hydration models and ASP sets is discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 636–654, 1999