Biomedical subjects

T Simonson

Publications and source records attributed to T Simonson.

24 records · Page 2Linked to original sources

PubMed1994

Properties of RecA-oligonucleotide complexes.

The interaction of RecA protein with short single-stranded oligonucleotides is characterised by flow linear dichroism (LD), isoelectric focusing (IEF) and electron microscopy (EM). From LD and EM it is evident that RecA forms long filaments with at least some 50 oligonucleotides in a 'train formation'. The tendency to form trains is substantially lower when an amino group is attached to the 5' end of the oligonucleotide, suggesting that the modification impairs protein-protein interactions at the interface between two oligomers. From LD it is also evident that no bridging occurs between RecA-oligonucleotide complexes containing more than one oligomer strand per RecA filament. This property make them manageable in polyacrylamide gels, hence allowing characterisation by IEF. RecA was found acidic with a pI of 5.0. The pI was not dependent on the presence of bound cofactor (ATP gamma S) and oligonucleotides suggesting that protonation of the protein readily occurs to compensate for the negative charges provided by bound cofactor and DNA.

Bacteriophage M13↗

PubMed1992

Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations.

Hydrophobic interactions between the S-peptide and S-protein in the ribonuclease-S complex are probed using molecular dynamics simulations and free energy calculations. Three successive mutations at the buried position Met13 are simulated: Met----Leu, Leu----Ile, and Ile----Val, for which X-ray structures and experimental thermodynamic data are available. The calculations give theoretical estimates of the changes in binding free energies associated with these mutations. The calculated free energy differences are small (0-1.6 kcal/mol), in agreement with experiment. However the simulated structures deviate significantly from the experimental ones (mean deviation approximately 1.5-2 A), and a large uncertainty in the calculated free energies (1-2 kcal/mol) arises from the multiple minimum problem. Indeed, multiple conformations are available to the side chains around the mutation site, and the sampling of dihedral rotamer transitions is limited, despite long simulations. Fluctuations within each local minimum give rise to a small statistical error. However the uncertainty due to multiple conformations is much greater than the uncertainty due to random statistical errors. In our work, an artificial cancellation of errors arose because we studied conformations of the RNase complex and of the S-peptide that were very similar. In general, the criterion for a precise simulation is not merely to reduce the random statistical error, as has been suggested, but rather to sample all the important local minima along the mutation pathway, and to reduce the statistical error for each one. Our calculations suggest that the packing changes associated with the mutations are energetically small and localized, and largely cancel when the complex and the S-peptide are compared. Solvation of the methionine side chain partial charges in the S-peptide and the complex appear to be energetically equivalent, so that removing them (as in Met13----Leu, Ile, Val) does not affect binding. Enthalpy and entropy changes could not be estimated reliably.

Computer Simulation↗

PubMed1992

Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk.

We use group theoretical methods to study the molecular dynamics of symmetric protein multimers in the harmonic or quasiharmonic approximation. The method explicitly includes the long-range correlations between protein subunits. It can thus address collective dynamic effects, such as cooperativity between subunits. The n lowest-frequency normal modes of each individual subunit are combined into symmetry coordinates for the entire multimer. The Hessian of the potential energy is thereby reduced to a series of blocks of order n or 2n. In the quasiharmonic approximation, the covariance matrix of the atomic oscillations is reduced to the same block structure by an analogous set of symmetry coordinates. The method is applied to one layer of the tobacco mosaic virus protein disk in vacuo, to gain insight into the role of conformational fluctuations and electrostatics in tobacco mosaic virus assembly. The system has 78,000 classical, positional, degrees of freedom, yet the calculation is reduced by symmetry to a problem of order 4,600. Normal modes in the 0-100 cm-1 range were calculated. The calculated correlations extend mainly from each subunit to its nearest neighbors. The network of core helices has weak correlations with the rest of the structure. Similarly, the inner loops 90-108 are uncorrelated with the rest of the structure. Thus, the model predicts that the dielectric response in the RNA-binding region is mainly due to the loops alone.

Binding Sites↗

PubMed1991

Intramolecular dielectric screening in proteins.

This paper investigates the microscopic mechanisms of charge screening by proteins. For this purpose, we introduce the generalized susceptibility of a protein in response to a point charge, which is a scalar quantity dependent on position within the protein. The contribution to the susceptibility from atomic polarizabilities, associated with electronic degrees of freedom, is found to be highly uniform. By contrast, that from dynamic dipolar relaxation, associated with nuclear degrees of freedom, varies greatly between different regions of the protein. We investigate the possible rôle of this variation in the activity of proteins that interact functionally with charged species, and we formulate and test the hypothesis that this variation is correlated to functional activity. Model calculations give encouraging support to this hypothesis. The protein's dielectric properties are represented by a standard model in which electronic relaxation is described by a set of atomic polarizabilities, and dipolar relaxation is treated as a perturbation to normal mode dynamics. The model yields the desired susceptibility in closed form. Its obvious limitations are discussed. It is applied to several test systems, and is compared to various continuum models. Four model alpha-helices are considered, three of which play a rôle in vivo in the binding of charged ligands. We show that the intramolecular screening, and its spatial variation, can indeed play a part in this binding. The electron transfer between ferri- and ferrocytochrome c is considered. The dielectric relaxation of each molecule, associated respectively with its oxidation or its reduction, is known to be directly related to the activation free energy for the electron transfer reaction. Our analysis of the dielectric susceptibility will thus permit an estimate of this activation free energy. We show that the relaxation of the atomic positions ("dipolar relaxation") contributes 1 kcal/mol to this activation free energy, and that the molecule achieves this low value by providing a low dipolar susceptibility throughout its central part. In this case, the spatial variation of the susceptibility has a clear functional rôle.

Amino Acid Sequence↗

PubMed1991

Microscopic theory of the dielectric properties of proteins.

This paper investigates the microscopic mechanisms of charge screening in proteins. The screening of an arbitrary perturbing charge density by a protein and its surrounding solution is characterized by a generalized susceptibility, which is approximately given by the mean dipole-dipole correlation matrix of the system. This susceptibility is a microscopic quantity; the sum of its matrix elements gives the macroscopic susceptibility of continuum electrostatics. When screening of a single perturbing point charge is considered, this susceptibility reduces to a scalar quantity, dependent on position within the protein. The contribution of the positional degrees of freedom of the protein atoms can be estimated from molecular dynamics simulations. This contribution gives rise to large spatial variations of the susceptibility, whose significance for protein function is discussed. The model is applied to the small alpha helix deca-alanine, and to the electron-transfer protein cytochrome c. The results agree qualitatively with previous normal mode calculations. The importance, and the large spatial variations, of charge screening by deca-alanine suggest that dielectric screening may play a role in the binding of charged ligands by helices. In cytochrome c, the dielectric susceptibility in response to a point charge is at a minimum in the central heme region, resulting in a lowering of the reorganization free energy for charge transfer to and from the heme.

Biophysical Phenomena↗

PubMedDate not supplied

Comparison of motor unit action potential characteristics and hand dominance using monopolar needle electrodes in the abductor pollicis brevis and abductor digiti minimi muscles.

This study examined specific electrical characteristics of voluntary single motor unit action potentials (SMUAPs): amplitude, duration, phase change, and rate of rise. These characteristics, which were detected from two intrinsic muscles of the hand--the abductor pollicis brevis and the abductor digiti minimi--were compared to hand dominance. Forty subjects participated in the study. Five characteristics were detected from each muscle using the quadrant technique while the subject produced a minimal isometric contraction. Based on results of an ANOVA [two-factor with replication] test, our study revealed no significant difference between muscles in the dominant and non-dominant hands. Descriptive statistics for each muscle characteristic are presented. This study has identified parameters for SMUAP characteristics detected in non-impaired individuals ranging in age from 20 to 43 years. The normative parameters serve as a valuable base from which one may examine potential neuronal damage from cumulative trauma disorders.

Action Potentials↗