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Biomedical subjects

M Karplus

Publications and source records attributed to M Karplus.

At least 289 records · Page 16Linked to original sources
PubMed1979

Picosecond dynamics of tyrosine side chains in proteins.

To probe the details of small amplitude motions in proteins, a dynamical analysis of the orientation fluctuations of two tyrosine side chains in the bovine pancreatic trypsin inhibitor is presented. Detailed results are given for the time history and correlation functions obtained for the ring motion from a molecular dynamics simulation of the entire protein. It is shown that even on a picosecond time scale orientational fluctuations of +/-30 degrees from the average position occur for the tyrosine rings in the interior of the protein. It is found that the Langevin equation is applicable to the ring torsional motion, which corresponds to that of an angular harmonic oscillator with near-critical damping. Two possible microscopic models for the observed damping effects are outlined. One of these, analogous to liquid behavior, is based on kinetic theory and takes account of the collisions which occur between atoms of the protein; the other, more analogous to solid behavior, involves the coupling among a large number of harmonic oscillators. The collisional model with parameters obtained from theoretical estimates leads to good agreement with the correlation functions from the dynamic simulation. However, the dephasing of harmonic oscillations can yield similar short-time results so that a distinction between the two models is difficult. The importance of damping effects on the motions involved in conformational transitions and enzymatic reactions is discussed.

Animals↗
PubMed1979

Monosomy 21: a possible stepwise evolution of the karyotype.

We describe a female infant with manifestations of complete monosomy for chromosome 21 intrauterine growth retardation, failure to thrive, craniofacial anomalies, arthrogryposis-like features, and psychomotor retardation. Chromosome analysis demonstrated mosaicism for three different cell lines in the various tissues examined; 45,XX,-21/46,XX,del(21)(q11)46,XX. The existence of these three lines suggests a possible explanation for the few cases of "complete monosomy 21" which have been reported.

Abnormalities, Multiple↗
PubMed1979

Dynamics of activated processes in globular proteins.

A procedure for the dynamical simulation of activated processes, such as ligand binding and enzymatic reactions, in a globular protein is outlined. Preliminary calculations of the transition state geometry and barrier crossing trajectories are presented for a model reaction, the rotation of an aromatic ring in the bovine pancreatic trypsin inhibitor. The results show that repulsive nonbonded interactions between the ring atoms and the atoms in the surrounding protein matrix determine the dynamical character of the reorientation process; the nonbonded interactions are the source of the rotational barrier and of the impulses that speed up or slow down the ring motion during the barrier crossings.

Animals↗
PubMed1978

Lack of limb motor asymmetry in the neonate.

Neonates were examined for evidence of lateralization of motor function. The stepping test was done and the foot that moved first was recorded. The reaction of both arms to avoid an obstacle was also tested. No evidence for lateralization was found. Previous studies in the neonate have shown asymmetry of anatomical structures subserving language, and functional asymmetry of auditory functions and head position. However, the development of limb handedness occurs only at a later age.

Age Factors↗
PubMed1977

Dynamics of folded proteins.

The dynamics of a folded globular protein (bovine pancreatic trypsin inhibitor) have been studied by solving the equations of motion for the atoms with an empirical potential energy function. The results provide the magnitude, correlations and decay of fluctuations about the average structure. These suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.

Aprotinin↗
PubMed1977

Mechanism of tertiary structural change in hemoglobin.

A reaction path is presented by which the effects of oxygen binding in hemoglobin are transmitted from a heme group to the surface of its subunit. Starting from the known deoxy geometry, it is shown by calculations with empirical energy functions and comparisons with available data how the change in heme geometry on ligation introduces a perturbation that leads to the tertiary structural alterations essential for cooperatively. It is found that there is little strain on the unliganded heme; instead, the reduced oxygen affinity of hemoglobin results from the strain on the liganded subunit in a tetramer with the deoxy quarternary structure.

Amino Acid Sequence↗
PubMed1976

Analysis of the interaction of organic phosphates with hemoglobin.

The interaction of organic phosphates with hemoglobin is studied by use of a simple thermodynamic approach. A model-independent analysis is employed to evaluate the accuracy of Adair constants determined in the presence of 2,3-diphosphoglycerate (DPG). The change of oxygen affinity in the presence of phosphates is related to the macroscopic phosphate binding constants of oxy- and deoxyhemoglobin and used to extract such binding constants from oxygen equilibrium measurements. The change of the Bohr effect in the presence of phosphates and the competitive binding of carbon dioxide and DPG are treated quantitatively. The binding of organic phosphates is incorporated into an allosteric model, in which the effect of phosphate on both tertiary and quaternary structure changes is included. By use of this model, the factors which can be responsible for the increased functional heterogeneity of alpha and beta chains in the presence of phosphates are clarified.

Binding Sites↗
PubMed1975

Analysis of cooperativity in hemoglobin. Valency hybrids, oxidation, and methemoglobin replacement reactions.

An allosteric model proposed previously for structure-function relations in hemoglobin is applied to the analysis of low- and high-spin valency hybrids. By assuming that the low-spin oxidized chains have the tertiary structure of oxygenated chains while the high-spin oxidized chains have a tertiary structure intermediate between that of deoxygenated and oxygenated chains, the model parameters associated with the different valency hybrids can be obtained, and their equilibrium properties can be estimated. The hybrid results are used also to provide an interpretation of methemoglobin and its ligand replacement reactions and of the oxidation-reduction equilibrium of normal hemoglobin. For the various systems studied it is found that the effects of pH and 2,3-diphosphoglycerate are in agreement with the model.

Allosteric Regulation↗
PubMed1975

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.

Conformational potentials of sidechains in the bovine pancreatic trypsin inhibitor have been studied with an empirical energy function. Calculated minimumenergy positions are in excellent agreement with the x-ray structure for sidechains in the core or at the surface of the protein; as expected, angles for sidechains that are directed out into the solvent do not agree with the calculated values. The contributions to the potentials are analyzed and compared with the potentials for the free amino acid. Although there is a large restriction in the available conformational space due to nonbonded interactions, the minimum energy positions in the protein are close to those of the free amino acid; the significance of this result is discussed. To estimate the effective barriers for rotation of the aromatic rings (tyrosine and phenylalanine), calculations are done in which the protein is permitted to relax as a function of the ring orientation. Thr resulting barriers, which are much lowere than the rigid rotation barriers, are used to evaluate the rotation rates; comparison is made with the available nuclear magnetic resonance data.

Animals↗