Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “MACROMOLECULAR SYSTEMS”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6Linked to original sources
PubMed1989

Allosteric formulation of thermal transitions in macromolecules, including effects of ligand binding and oligomerization.

We examine the effects of concentration (aggregation), buffers, and ligation, under conditions of either constant ligand activity or limited total amount of ligand, upon thermal denaturation of macromolecules as measured by scanning calorimetry. In doing so we utilize and extend an earlier generalized allosteric treatment [S. J. Gill, B. Richey, G. Bishop, and J. Wyman (1985) Biophys. Chem. 21, 1-14], applicable to ligand binding, enthalpy changes, and volume changes in a macromolecular system. The approach is contrasted with formulations based on the idea of structural domains. We show how information from the full scanning calorimetric curves can be utilized in arriving at and testing appropriate models for observed behavior in selected examples.

Allosteric Regulation↗
PubMed2003

Thermodynamics of specific protein-RNA interactions.

Description of the recognition specificity between proteins and nucleic acids at the level of molecular interactions is one of the most challenging tasks in biophysics. It is key to understanding the course and control of gene expression and to the application of the thus acquired knowledge in chemotherapy. This review presents experimental results of thermodynamic studies and a discussion of the role of thermodynamics in formation and stability of functional protein-RNA complexes, with a special attention to the interactions involving mRNA 5' cap and cap-binding proteins in the initiation of protein biosynthesis in the eukaryotic cell. A theoretical framework for analysis of the thermodynamic parameters of protein-nucleic acid association is also briefly surveyed. Overshadowed by more spectacular achievements in structural studies, the thermodynamic investigations are of equal importance for full comprehension of biopolymers' activity in a quantitative way. In this regard, thermodynamics gives a direct insight into the energetic and entropic characteristics of complex macromolecular systems in their natural environment, aqueous solution, and thus complements the structural view derived from X-ray crystallography and multidimensional NMR. Further development of the thermodynamic approach toward interpretation of recognition and binding specificity in terms of molecular biophysics requires more profound contribution from statistical mechanics.

Animals↗
PubMed1978

Analysis of ligand binding curves in terms of species fractions.

The ligand binding curve for a macromolecular system presents the average number of ligand molecules bound per macromolecule as a function of the chemical potential or the logarithm of the ligand concentration. We show that various observable properties of this curve, for example its asymptotes and derivatives, are expressible in terms of linear combinations of the mole fractions alphai of macromolecules binding i molecules of ligand. Whenever enough such properties of the binding curve are known, the linear equations in alphai can be solved to give the mole fractions of each of the various macromolecular species. An application of these results is that a Hill plot for hemoglobin-ligand equilibrium where the asymptotes approach unit slope can be made to yield the four Adair constants by a simple algebraic method. A second use is that a knowledge of the first and second derivatives of the binding curve at points along the curve can yield the species fractions as functions of the degree of saturation without direct knowledge of the ligand binding constants. These methods are illustrated by some numerical examples.

Binding Sites↗
PubMed1986

Autoradiographic localization of subcomponents of the macromolecular GABA receptor complex.

The autoradiographic localization of subcomponents of the gamma-aminobutyric acid (GABA) receptor-chloride ionophore complex has provided insight into the distribution of this macromolecular system. GABA inhibits neurons by preferentially increasing the permeability of the affected membrane to chloride ions. This inhibition can be modified by the presence of other substances which bind to the GABA receptor complex. Autoradiographic localization of specific receptor subtypes associated with this complex has been accomplished in the central nervous system. This type of analysis has been performed on high and low affinity GABAA, benzodiazepine (BZ; both BZ1 and BZ2) and convulsant sites. These receptor sites are situated in distinct brain regions and co-exist in several areas. Other receptor subtypes, which may be influenced by the presence of GABA, can be analyzed for comparison in order to define regions of the brain where GABA may be exerting independent effects (i.e., those not associated with chloride channels). Microscopic localization of receptor sites indicates specific areas to investigate in further studies concerning the characterization of subcomponents of the macromolecular GABA complex associated with chloride ion channels.

Animals↗
PubMed1994

Quantitative analysis in the characterization and optimization of protein crystal growth.

Protein crystal growth often depends on the combination of many different factors. Some affect protein solubility directly; others may act indirectly by causing conformational changes. Systematic characterization of these factors can be important for generating good crystals. It can also provide useful insight into the biochemical behavior of the protein being crystallized. Here we focus on statistical methods to achieve these two objectives. (1) Characterization of a protein system by analyzing patterns of crystal polymorphism under different levels of biochemical parameters, such as ligands and pH. Tests of the reproducibility of crystal growth experiments indicate that quantitative scales of crystal quality can be statistically significant. Analysis of variance for a replicated, full-factorial design in which four factors were tested at two levels has been used to demonstrate highly significant, biochemically relevant, two-factor interactions strongly implicating pH and ligand-dependent conformational changes. (2) Optimization of crystal growth via response-surface methods. 'Minimum predicted variance' designs provide for efficient response-surface experiments aimed at constructing quadratic models in several dimensions. We have used such models to improve crystal size and quality significantly for three forms of Bacillus stearothermophilus tryptophanyl-tRNA synthetase. In one case we can now avoid having to increase the size by repeated seeding, a difficult procedure that also produces unwanted growth of satellite crystals. Graphs of two-dimensional level surfaces reveal a number of ridges, where the same result is obtained for many combinations of the factors usually varied when trying to improve crystals. An important inference is that it may be better to sample simultaneously for the effects of protein concentration and supersaturation. For a system involving only one crystallizing agent, supersaturation can be approximated as the product of protein and precipitant concentrations. Use of this search direction significantly improves the performance of response-surface experiments. Advantages of growing crystals at stationary points of their response surfaces include better crystals and higher reproducibility, since crystal growth at stationary points is insulated from the deleterious effects of experimental fluctuations. This arises because the derivatives of the response are by definition zero with respect to the experimental variables. Quantitative analysis of appropriately designed crystal growth experiments can thus be a powerful way to characterize complex and interacting biochemical dependencies in macromolecular systems and optimize parameters important to the crystallography.

Journal Article↗
PubMed2003

MC-PHS: a Monte Carlo implementation of the primary hydration shell for protein folding and design.

A primary hydration shell (PHS) approach is developed for Monte Carlo simulations of conformationally rich macromolecular systems in an environment that efficiently captures principal solvation effects. It has been previously demonstrated that molecular dynamics using PHS is an efficient method to study peptide structure and dynamics in aqueous solution. Here, we extend the PHS approach to Monte Carlo simulations, whereby a stable shell of water molecules is maintained with a flexible, nonspherical, half-harmonic potential, tuned to maintain a constant restraining energy, with the difference between the restraint and shell energies used to dynamically adjust the shell radius. Examination of the shell and system size dependence of the restraining potential reveals its robustness. Moreover, its suitability for biomolecular simulations is evaluated using small spheres of water, hydration properties of small biological molecules, and configurational sampling of beta-hairpin pentapeptide YPGDV. This method, termed MC-PHS, appears to provide efficient representation of dominant solvation effects and should prove useful in the study of protein folding and design.

Amino Acids↗
PubMed2005

Tensile creep properties of interpenetrating networks containing gelatin and poly(ethylene glycol) diacrylate.

The tensile creep properties of an interpenetrating networks (IPN) system containing polyanionic ethylenediaminetetraacetic dianhydride (EDTAD)-modified gelatin and poly(ethylene glycol) diacrylate (PEGdA) of 600 or 2000 Da at various weight ratios were determined under different pH and load levels. A computerized creep testing device was designed following ASTM D2990 and validated to establish the environment-dependent structure-function relationship of IPNs. IPNs containing PEGdA 2000 Da or EDTAD-modified gelatin showed less strain than those formulated with PEGdA 600 Da or unmodified gelatin, respectively. IPN formulated with 40 wt% gelatin showed higher strain than those with 50 or 30 wt% gelatin. Increasing strain in IPN was observed with increasing load level. IPN strain was higher at pH 7 when compared to pH 4 or 10. The creep characteristics of this complex macromolecular system are dependent on both environmental and composition factors.

Anhydrides↗
PubMedDate not supplied

Polyester dendritic systems for drug delivery applications: in vitro and in vivo evaluation.

High molecular weight polymers (> 20 000 Da) have been widely used as soluble drug carriers to improve drug targeting and therapeutic efficacy. Dendritic polymers are exceptional candidates for the preparation of near monodisperse drug carriers due to their well-defined structure, multivalency, and flexibility for tailored functionalization. We evaluated various dendritic architectures composed of a polyester dendritic scaffold based on the monomer unit 2,2-bis(hydroxymethyl)propanoic acid for their suitability as drug carriers both in vitro and in vivo. These systems are both water soluble and nontoxic. In addition, the potent anticancer drug, doxorubicin, was covalently bound via a hydrazone linkage to a high molecular weight 3-arm poly(ethylene oxide)-dendrimer hybrid. Drug release was a function of pH, and the release rate was more rapid at pH < 6. The cytotoxicity of the DOX-polymer conjugate measured on multiple cancer lines in vitro was reduced but not eliminated, indicating that some active doxorubicin was released from the drug polymer conjugate under physiological conditions. Furthermore, biodistribution experiments show little accumulation of the DOX-polymer conjugate in vital organs, and the serum half-life of doxorubicin attached to an appropriate high molecular weight polymer has been significantly increased when compared to the free drug. Thus, this new macromolecular system exhibits promising characteristics for the development of new polymeric drug carriers.

Animals↗
PubMed2005

Ribosome builder: a software project to simulate the ribosome.

The Ribosome Builder is a software project that provides tools and techniques to create dynamic models of macromolecular systems from the rapidly growing numbers of atomic structural models. It includes a computer program that allows the user to assemble the multiple molecular components within a 3D space and to define the hypothetical interactions of these components with the initial goal of understanding protein translation at an atomic level of detail. The program employs a simplified molecular dynamics forcefield that can simulate the long time-scale events, such as docking of translation factors and mRNA translocation. An embedded scripting language and Application Programming Interface (API) enable the creation of Steered Molecular Dynamics (SMD) simulations through the programmable application of external forces and torques on atoms and bonds. A graphical interface is provided for displaying and interacting with models, recording movies of molecular dynamics movements, and creating annotated 3D simulations of complex macromolecular events. Initial applications of the project include simulation of tetraloop folding, docking of an mRNA on the 30S subunit and a schematic simulation of the translation elongation cycle. The program is an open source project released under the GNU public license.

Computer Simulation↗
PubMed1988

Frequency spectrum of enthalpy fluctuations associated with macromolecular transitions.

A multifrequency calorimeter has been designed to measure the amplitude and time regime of the enthalpic fluctuations associated with structural or conformational transitions in biological macromolecular systems. The heat capacity function at constant pressure is directly proportional to the magnitude of the enthalpic fluctuations in a system. Biological macromolecules undergo thermally induced transitions of different kinds. Within the transition region, these systems exhibit relatively large enthalpy fluctuations that give rise to the characteristic peaks observed by conventional differential scanning calorimetry. The multifrequency calorimeter developed in this laboratory has been designed to measure the frequency spectrum of the enthalpy fluctuations, thus allowing us to estimate thermodynamic parameters as well as relaxation times. This information is obtained from the attenuation in the amplitude or phase-angle shift of the response of the system to a periodic temperature oscillation. This instrument has been used to study the gel-liquid crystalline transition of phosphatidylcholine bilayers. The frequency-temperature response surface for large dimyristoyl phosphatidylcholine vesicles has been measured in the frequency range 0.04-1 Hz. The data are consistent with two enthalpic relaxation processes with time constants on the order of 3.8 s and 80 ms at the midpoint of the main gel-liquid crystalline transition.

Calorimetry, Differential Scanning↗
PubMed2001

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels.

Algorithms↗
PubMed2003

Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics.

Oligomerization and ligand binding are thermodynamically cooperative processes in many biochemical systems, and the mechanisms giving rise to cooperative behavior are generally attributed to changes in structure. In glycopeptide antibiotics, however, these cooperative processes are not accompanied by significant structural changes. To investigate the mechanism by which cooperativity arises in these compounds, fully solvated molecular dynamics simulations and quasiharmonic normal-mode analysis were performed on chloroeremomycin, vancomycin, and dechlorovancomycin. Configurational entropies were derived from the vibrational modes recovered from ligand-free and ligand-bound forms of the monomeric and dimeric species. Results indicate that both ligand binding and dimerization incur an entropic cost as vibrational activity in the central core of the antibiotic is shifted to higher frequencies with lower amplitudes. Nevertheless, ligand binding and dimerization are cooperative because the entropic cost of both processes occurring together is less than the cost of these processes occurring separately. These reductions in configurational entropy are more than sufficient in magnitude to account for the experimentally observed cooperativity between dimerization and ligand binding. We conclude that biochemical cooperativity can be mediated through changes in vibrational activity, irrespective of the presence or absence of concomitant structural change. This may represent a general mechanism of allostery underlying cooperative phenomena in diverse macromolecular systems.

Anti-Bacterial Agents↗
PubMed2000

Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.

Residual dipolar couplings for pairs of proximate magnetic nuclei in macromolecules can easily be measured using high-resolution NMR methods when the molecules are dissolved in dilute liquid crystalline media. The resulting couplings can in principle be used to constrain the relative orientation of molecular fragments in macromolecular systems to build a complete structure. However, determination of relative fragment orientations based on a single set of residual dipolar couplings is inherently hindered by the multi-valued nature of the angular dependence of the dipolar interaction. Even with unlimited dipolar data, this gives rise to a fourfold degeneracy in fragment orientations. In this Communication, we demonstrate a procedure based on an order tensor analysis that completely removes this degeneracy by combining residual dipolar coupling measurements from two alignment media. Application is demonstrated on (15)N-(1)H residual dipolar coupling data acquired on the protein zinc rubredoxin from Clostridium pasteurianum dissolved in two different bicelle media.

Bacterial Proteins↗
PubMed1987

Temperature and macromolecular structure and function.

Stability is frequently a knife-edge phenomenon and it is this aspect which is both essential for the effective involvement of macromolecules in the living cell and also provides the basis for the sensitivity of some macromolecular systems to temperature. The response of proteins and nucleic acids is relatively simple at the phenomenological level, with rather sharp 'melting' transitions occurring. Since however the thermodynamic stability of both depends on the cooperation of a variety of non-covalent interactions which are qualitatively well understood but quantitatively difficult to assess, the full understanding and prediction of structural stability still evades us. We shall consider the effects of temperature on the different non-covalent interactions and how far these can account for protein and nucleic acid denaturation at elevated temperatures and also the cold inactivation of proteins. The latter has recently been shown to involve unsuspected complications in terms of protein conformational change. The increased stability of proteins and nucleic acids from thermophiles will be discussed. Stability is important not only in native folded proteins but also with respect to intermediate structures which occur during the folding of the newly synthesized polypeptide chain into the native, active protein. Through studies of protein folding the molecular basis of the phenomenon of temperature sensitive synthesis has been revealed. Given a stable molecular structure, its function will frequently be subject to variation with temperature. The deceptively simple temperature dependence of enzyme activity will involve the non-covalent interactions considered above for interaction between enzyme and substrate and for stability of the transition state complex. This complexity again makes the temperature dependence difficult to interpret. Further, the fact that proteins are dynamic structures is becoming recognized as an important feature factor in determining function. A balance has to be struck between on the one hand dynamic mobility which is essential for catalytic activity and on the other thermodynamic stability which holds the molecule in a potentially functional conformation under the given conditions of temperature and pressure. Readjustment of thermostability stability, as in thermophiles (or vice versa?), must also involve readjustment of dynamic mobility.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1999

Simulation of peptide folding with explicit water--a mean solvation method.

A new approach to efficiently calculate solvent effect in computer simulation of macromolecular systems has been developed. Explicit solvent molecules are included in the simulation to provide a mean solvation force for the solute conformational search. Simulations of an alanine dipeptide in aqueous solution showed that the new approach is significantly more efficient than conventional molecular dynamics method in conformational search, mainly because the mean solvation force reduced the solvent damping effect. This approach allows the solute and solvent to be simulated separately with different methods. For the macromolecule, the rigid fragment constraint dynamics method we developed previously allows large time-steps. For the solvent, a combination of a modified force-bias Monte Carlo method and a preferential sampling can efficiently sample the conformational space. A folding simulation of a 16-residue peptide in water showed high efficiency of the new approach.

Computer Simulation↗
PubMedDate not supplied

Theory and applications of the generalized Born solvation model in macromolecular simulations.

Generalized Born (GB) models provide an attractive way to include some thermodynamic aspects of aqueous solvation into simulations that do not explicitly model the solvent molecules. Here we discuss our recent experience with this model, presenting in detail the way it is implemented and parallelized in the AMBER molecular modeling code. We compare results using the GB model (or GB plus a surface-area based "hydrophobic" term) to explicit solvent simulations for a 10 base-pair DNA oligomer, and for the 108-residue protein thioredoxin. A slight modification of our earlier suggested parameters makes the GB results more like those found in explicit solvent, primarily by slightly increasing the strength of NH [bond] O and NH [bond] N internal hydrogen bonds. Timing and energy stability results are reported, with an eye toward using these model for simulations of larger macromolecular systems and longer time scales.

Computer Simulation↗
PubMed1991

Metabolic enantiomeric interactions: the inhibition of human (S)-warfarin-7-hydroxylase by (R)-warfarin.

Inhibition of the metabolism of (S)-warfarin, the more pharmacologically active enantiomer of the racemic drug, by (R)-warfarin was investigated in microsomes obtained from three human livers. In each case the production of both (S)-6- and (S)-7-hydroxywarfarin was found to be competitively inhibited by (R)-warfarin. The KiS for inhibition of (S)-6- and (S)-7-hydroxylation by (R)-warfarin ranged from 7.0 to 8.4 microM and from 6.0 to 6.9 microM, respectively, while the KmS for the 6- and 7-hydroxylation of (S)-warfarin ranged from 3.6 to 3.8 microM and from 3.3 to 3.9 microM, respectively. In contrast, except for the 4'-hydroxylation pathway (S)-warfarin was found to be a weak inhibitor of the metabolism of (R)-warfarin. Possible implications of these findings include the following: (1) the kinetic parameters defining the interactions of two enantiomers of a racemic drug with the cytochrome P-450s or other macromolecular systems in the living organism can only be properly defined from experiments with the pure enantiomers, (2) an enantiomer of a racemic drug may contribute significantly to biological effect not by its inherent activity but by altering the pharmacokinetics of the eutomer, and (3) enantiomeric interactions are not easily detected unless directly sought and may be relatively common.

Aryl Hydrocarbon Hydroxylases↗
PubMed2002

Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method.

The pure quantum mechanics method, called Local Self-Consistent Field (LSCF), that allows to optimize a wave function within the constraint that some predefined spinorbitals are kept frozen, is discussed. These spinorbitals can be of any shape, and their occupation numbers can be 0 or 1. Any post-Hartree-Fock method, based on the restricted or unrestricted Hartree-Fock Slater determinant, and Kohn-Sham-based DFT method are available. The LSCF method is easily applied to hybrid quantum mechanics/molecular mechanics (QM/MM) procedure where the quantum and the classical parts are covalently bonded. The complete methodology of our hybrid QM/MM scheme is detailed for studies of macromolecular systems. Not only the energy but also the gradients are derived; thus, the full geometry optimization of the whole system is feasible. We show that only specific force field parameters are needed for a correct description of the molecule, they are given for some general chemical bonds. A careful analysis of the errors induced by the use of molecular mechanics in hybrid computation show that a general procedure can be derived to obtain accurate results at low computation effort. The methodology is applied to the structure determination of the crambin protein and to Menshutkin reactions between primary amines and chloromethane.

Journal Article↗