Low-frequency vibrations in alpha-helices: helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories.

We present an approach to the analysis of low-frequency (0-200 cm-1) alpha-helix vibrations in molecular dynamics simulations. The approach employs the P-Curves algorithm [H. Sklenar, C. Etchebest, and R. Lavery, (1989) Proteins: Structure, Function and Genetics, Vol. 6, pp. 46-60] to determine the helical axis and a set of helicoidal parameters describing the axis curvature and the position of the repeating units with respect to the axis and each other. The vibrations are analyzed in terms of time correlation functions of the fluctuations of P-Curves parameters and their Fourier transforms. Simulations of polyalanine and myoglobin are analyzed. For polyalanine, global twisting, bending, and stretching vibrations are found at 11, 20, and 40 cm-1, respectively. In myoglobin, the spectra of the global helix vibrations are qualitatively different from those of polyalanine and considerably more complicated. Local vibrations of individual amino acid units in the helix backbones are also analyzed with P-Curves and compared.

Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin.

The contribution of rigid-body motions to the atomic trajectories in a 100 ps molecular dynamics simulation of deoxymyoglobin is examined. Two types of rigid-body motions are considered: one in which the helices are rigid units and one in which the side-chains are rigid units. Using a quaternion-based algorithm, fits of the rigid reference structures are made to each time frame of the simulation to derive trajectories of the rigid-body motions. The fitted trajectories are analysed in terms of atomic position fluctuations, mean-square displacements as a function of time, velocity autocorrelation functions and densities of states. The results are compared with the corresponding quantities calculated from the full trajectory. The relative contribution of the rigid helix motions to the helix atom dynamics depends on which quantity is examined and on which subset of atoms is chosen; rigid-helix motions contribute 86% of the rms helix backbone atomic position fluctuations, but 30% of the helix atom (backbone and side-chain) mean square displacements and only 1.1% of total kinetic energy. Only very low-frequency motions contribute to the rigid-helix dynamics; the rigid-body analysis allows characteristic rigid-helix vibrations to be identified and described. Treating the side-chains as rigid bodies is found to be an excellent approximation to both their diffusive and vibrational mean-square displacements: 96% of side-chain atom mean-square displacements originate from rigid side-chain motions. However, the errors in the side-chain atomic positional fits are not always small. An analysis is made of factors contributing to the positional error for different types of side-chain.

The effect of point mutations on energy profiles in a model of the nicotinic acetylcholine receptor (AChR) channel.

Energy profiles are calculated, using energy optimization computations, for a sodium cation in the AChR channel and four of its mutants, alpha E241D, beta E247Q, delta E255Q and alpha E241Q, using the model developed previously. The relative energy location of the calculated profiles confirms and specifies the role of each of the Glu residues found in the anionic ring at the bottom of the MII helices. The structural analysis of the results allows the understanding of the differences observed in the conductances for the wild-type and mutant alpha E241D, or for the mutants beta E247Q and delta E255Q in spite of the identity of the global charge of both channels in each couple. The striking correlation observed between the average relative energy location of the profiles and the conductance data appears to provide confirmation of the essential structural features adopted in the model, in particular the inclusion of the Glu(Gln in gamma)-Lys residues in the alpha-helical stretch of the MII helices and the overall location of the internal residues.

A possible model for the inner wall of the acetylcholine receptor channel.

A structural model of the inner wall of the acetylcholine receptor (AChR) channel is developed using assumptions derived from the results of the recent labelling experiments of the MII helices by noncompetitive blockers. The assumption of steric blocking of the channel by chlorpromazine (CPZ) in the neighbourhood of the labelled serines imposes the MII helices to be in contact at this level and allows the calculation of their minimal interaxial distance. The assumption that CPZ diffuses to this position through the upper crowded part of the channel imposes that the helices are more distant in this region and permits the determination of a tilt of about 7 degrees with respect to the central axis. Electrostatic potentials are used to demonstrate the effect of the charged residues at the exit of the pore. A discussion is given on the possible aptitude of MI to satisfy the contacts necessary with the MII/s at the different heights of the model.

Energy profiles in the acetylcholine receptor (AChR) channel. The MII-helix model and the role of the remaining helices.

It is demonstrated by theoretical computations that no favorable energy profile for cation transfer can be obtained in a model of the AChR channel constructed with the sole five MII helices of the inner wall. A favorable profile is obtained upon including the effect of the remaining helices of the five subunits. The decisive role, for the exit of the ion, of the charged residues situated at the N-terminal of the MII segments, established before, is underlined further. The role of the other elements of the channel wall (peptide carbonyl oxygens, hydrocarbon residues and polar side chains) is analyzed.

Conformation and pairing properties of the N-terminal fragments of trichorzianine and alamethicin: a theoretical study.

Energy optimizations are carried out on the N-terminal fragment of trichorzianine in comparison to that of alamethicin. The results indicate that the helical character of the (Ac...Pro13) sequence of trichorzianine (TA IIIc) is essentially alpha with a bend in the helix axis in the end proline region, a structure comparable to the optimal alpha-helical structure of the corresponding segment (Ac...Pro14) of alamethicin AI. However, two weak n----n + 3 interactions coexist in trichorzianine with the alpha-helical n----n + 4 hydrogen bonds. The possible role of the glutamine side-chains in pairing such segments together is considered.

Theoretical study of the packing of alpha-helices into possible transmembrane bundles. Sequences including alanines, leucines and serines.

Energy optimizations are carried out on packages of two and five alpha-helices containing leucines on their faces of contact and made otherwise of alanines. The effect of these bulky side-chains on the optimal arrangements is analysed and compared to the results previously obtained for pure poly(L-alanine) packages; the essential pairing properties are conserved (near antiparallelism, preponderous role of the non-bonded interactions, possibility of existence of parallel pairs); five alpha-helices made of 8 alanines and 6 leucines (three on each interface) can pack in different stable P5L bundles including various holes, according to the tilt and relative sliding of the helices. Substitution of serines to the alanines lying on the inner wall affects very little the interhelix packing. The seryl side chains adapt their conformation at best to their surroundings. The P5L packages can be used to represent individual subunits arranged in 'superbundles' around a central pit in a channel-forming protein.

Theoretical study of potential ion-channels formed by a bundle of alpha-helices: effect of the presence of polar residues along the channel inner wall.

In a channel-forming bundle of five alpha-helices of poly-L-alanine, the replacement of all the alanyl side-chains lining the inner wall by serines is shown, by energy optimization, to produce only small modifications of the packing. The stability of the bundle is larger than that of the pure alanyl package, owing to hydrogen bonding between serine hydroxyls and carbonyl oxygens. The energy profile for sodium as well as the water-channel interactions are favored by the presence of the OH groups and by the lability of the seryl side chains. The possible general significance of the results is suggested.

Specificity in carcinogen-DNA interaction: a theoretical exploration of the factors involved in the effect of neighboring bases on N-methyl-N-nitrosourea alkylation of DNA.

Recent experimental studies indicate that in a polynucleotide chain neighboring bases have a significant effect on the relative alkylation of O6 or N7 of guanine by N-methyl-N-nitrosourea (MNU). This paper provides a theoretical exploration of this phenomenon in terms of an appropriate index of reactivity, called accessible surface integrated field (ASIF), introduced recently for the very sake of accounting for specificity or selectivity in drug-macromolecule interaction. The detailed analysis indicates that in the present case the observed variations in relative reactivity are attributable essentially to parallel variations in the accessibilities to the target atoms.

A theoretical study of the effect of structural variations on the biochemical reactivity of yeast tRNAPhe and yeast tRNAAsp.

The ASIF index which combines both steric and electronic factors is applied to the comparative study of the reactivity of yeast tRNAAsp and yeast tRNAPhe using the coordinates deduced from their crystal structures. The results compared with the known experimental reactivities in solution are somewhat less perfect for tRNAAsp than for tRNAPhe. The reasons for this situation are probably related to the differences existing between the structures of tRNAAsp in the crystal and in solution.