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M Karplus

Publications and source records attributed to M Karplus.

At least 253 records · Page 14Linked to original sources
PubMed1983

Hemoglobin tertiary structural change on ligand binding. Its role in the co-operative mechanism.

Analysis of the tertiary structural alterations in hemoglobin induced by ligand binding demonstrates that an allosteric core composed of the heme, histidine F8, the FG corner and part of the F-helix plays an essential role in co-operativity. This conclusion is based on structural and spectroscopic data and theoretical studies of hemoglobin chains. The methodology employed in the calculations is presented with details of the empirical energy function. Energy minimized structures of the unliganded hemoglobin chains, which serve as reference systems for the analysis, are described. To determine the structural changes induced by ligand binding, the effects of Fe--N bond shortening and of heme translation and tilting perturbations are examined. Energy minimization in the presence of the perturbations serves to provide information concerning the globin structural modifications produced by them. The validity of the results is supported by comparisons with the X-ray data of Anderson, Pulsinelli, Baldwin and Chothia on tertiary changes in the hemoglobin subunits. Internal to the allosteric core, there appear to be two stable positions for its elements: one of these corresponds to the liganded and the other to the unliganded species. The unliganded geometry fits without strain into the deoxy tetramer, while the liganded one fits without strain into the oxy tetramer. On ligation of a subunit in the deoxy tetramer, the structural changes within the allosteric core are in the direction of those found in going from the unliganded deoxy to the liganded oxy system, although they are reduced by the presence of constraints due to the other subunits in the deoxy tetramer. In addition, the quaternary constraints in the deoxy tetramer prevent the large overall displacement of the allosteric core that occurs in the transition to the liganded oxy tetramer. The coupling between the changes internal to the allosteric core, produced on ligation and the overall displacement of the core that accompanies the quaternary transition, is an essential element of the co-operative mechanism. As shown in previous work (Gelin & Karplus, 1977), the proximal histidine serves as the link between the position of the heme and the F-helix; the asymmetric orientation of the histidine in the deoxy structure, coupled with contributions from other heme-protein interactions, appears to initiate the tertiary structural changes induced by ligand binding. The reduced oxygen affinity of hemoglobin results not from tension on the heme in the unliganded structure (there is none) but instead from strain in the liganded subunit of the tetramer within the deoxy quaternary structure.(ABSTRACT TRUNCATED AT 400 WORDS)

Allosteric Site↗
PubMed1983

Molecular anatomy of the antibody binding site.

The binding region of immunoglobulins, which includes the portion of the molecule having the most variability in its amino acid sequence, is shown to have a surprisingly constant structure that can be characterized in terms of a simple, well-defined model. The binding region is composed of the antigen combining site plus its immediate vicinity and arises by noncovalent association of the light and heavy chain variable domains (VL and VH, respectively). The antigen combining site itself consists of six polypeptide chain segments ("hypervariable loops") which comprise some 80 amino acid residues and are attached to a framework of VL and VH beta-sheet bilayers. Having analyzed refined x-ray crystallographic coordinates for three antigen-binding fragments (Fab KOL (Marquart, M., Deisenhofer, J., and Huber, R. (1980) J. Mol. Biol. 141, 369-391), MCPC 603 (Segal, D., Padlan, E. A., Cohen, G. H., Rudikoff, S., Potter, M., and Davies, D. R. (1974) Proc. Natl. Acad. Sci. U. S. A. 71, 4298-4302), and NEW (Saul, F. A., Amzel, L. M., and Poljak, R. J. (1978) J. Biol. Chem. 253, 585-597] we use the results to introduce a general model for the VL-VH interface forming the binding region. The region consists of two closely packed beta-sheets, and its geometry corresponds to a 9-stranded, cylindrical barrel of average radius 0.84 nm with an average angle of -53 degrees between its two constituent beta-sheets. The barrel forms the bottom and sides of the antigen combining site. The model demonstrates that the structural variability of the binding region is considerably less than was thought previously. Amino acid residues which are part of the domain-domain interface and appear not to be accessible to solvent or antigen contribute to antibody specificity.

Amino Acid Sequence↗
PubMed1983

Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study.

A molecular dynamics simulation of lysozyme is used to examine the fluorescence depolarization of tryptophan residues on the picosecond time scale. The calculated time dependence of fluorescence emission anisotropy for the six tryptophans in lysozyme exhibits a wide variety of motional behavior that should correspond to the range expected more generally for tryptophan residues in proteins. It is found that some tryptophans are highly mobile with a large fluorescence anisotropy decay on the picosecond time scale while others are essentially rigid due to the presence of the protein matrix. Further, it is demonstrated that correlations among the internal degrees of freedom (e.g., dihedral angles) play an important role in the observed decay behavior; this suggests that care has to be used in interpreting experimental results in terms of simple motional models. Because the available experimental time resolution is limited to the nanosecond time scale, only the effective zero-time anisotropy can be compared with the calculated values. The results suggest that the study of fluorescence depolarization with femtosecond lasers would provide new insights into the short time dynamics of amino acid side chains in proteins.

Fluorescence Polarization↗
PubMed1983

Discordant Hirschsprung's disease in monozygotic twins.

Two pairs of twins are being reported where monozygocity was supported by the observed sharing of a single and common placenta and by ABO and HLA identity. Only one of each pair of twins was affected by long-segment Hirschsprung's disease; the other twins were entirely normal. Discordant Hirschsprung's disease in monozygotic twins is very rare. The etiology in such cases is influenced by genetic or by environmental intrauterine factors rather than by postnatal influences, as suggested elsewhere.

Diseases in Twins↗
PubMed1983

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.

A normal mode analysis making use of an empirical potential function including local and nonlocal (nonbonded) interactions is performed for the bovine pancreatic trypsin inhibitor in the full conformational space of the molecule (1,740 degrees of freedom); that is, all bond lengths and angles, as well as dihedral angles, are included for the 580-atom system consisting of all heavy atoms and polar hydrogens. The heavy-atom frequency spectrum shows a dense distribution between 3 and 1,800 cm-1, with 350 modes below 216 cm-1. Most of the low-frequency modes, of which many have significant anharmonic character, are found to be delocalized over the protein. The root-mean-square amplitudes of the atomic fluctuations are calculated at 300 K from the normal modes and compared with those obtained from a solution molecular dynamics simulation based on the same potential function; very good agreement is obtained for the variation in the main-chain fluctuations as a function of residue number, though larger differences occur for the side chains. The fluctuations are generally, though not always, dominated by frequencies below 30 cm-1, in accord with the results of the dynamics simulation. The vibrational contributions to the thermodynamic properties of the protein are calculated as a function of temperature; the effects of perturbations on the spectrum, suggested for ligand or substrate binding, are examined. The analysis demonstrates that, in spite of the anharmonic contributions to the potential, a normal mode description can provide useful results concerning the internal motions of proteins.

Animals↗
PubMed1983

Structure-specific model of hemoglobin cooperativity.

A generalization of the Szabo-Karplus statistical mechanical model for hemoglobin cooperativity is formulated. The model fits the available thermodynamic and spectroscopic data with assumptions that are consistent with structural results and empirical energy function calculations. It provides a mechanism of hemoglobin cooperativity that is a generalization of the proposals of Monod, Wyman, and Changeux and of Perutz. The role of nonsalt-bridge related sources of constraints on ligand affinity and the mode of salt-bridge coupling to tertiary-quaternary structural changes are examined within the framework of the model. Analysis of proton release data for a range of pH values indicates that a pH-independent part of cooperativity must be present. The pH dependence of the first and last Adair constants point to partial linkage of salt bridges to ligation in the deoxy state and to a destabilized intra-beta-chain salt bridge in the unliganded oxy state.

Animals↗
PubMed1983

Solution NMR studies of intact lambda repressor.

Using a combination of two and one-dimensional NMR spectroscopy, it is shown that in the intact bacteriophage lambda repressor, the N-terminal domain assumes the same global structure as when it remains isolated. It is further shown that the N-terminal domain is only loosely attached to the C-terminal domain in the intact repressor.

DNA-Binding Proteins↗
PubMed1983

Dynamics of DNA oligomers.

The techniques of molecular and harmonic dynamics are used to study the internal mobility of three double-stranded DNA hexamers. A 60 ps molecular dynamics simulation and a normal mode description of d(CpGpCpGpCpG)2 in the B conformation characterize the atomic fluctuations of this structure. A comparison between the two approaches validates the harmonic results at room temperature. Detailed examination of the normal modes indicates that only the low-frequency modes are needed to determine atomic fluctuations. A harmonic analysis is made of d(CpGpCpGpCpG)2 in the Z conformation and of d(TpApTpApTpA)2 in the B conformation using only the low-frequency modes. The atomic fluctuations of the three alternating pyrimidine-purine helices are compared and the dependence on conformation and sequence are discussed. The insights which theoretical calculations can provide for the interpretation of experimental results are explored.

Base Sequence↗
PubMed1982

Protein dynamics in solution and in a crystalline environment: a molecular dynamics study.

The effect of a solvent and a crystalline environment on the dynamics of proteins is investigated by the method of computer simulation. Three 25-ps molecular dynamics simulations at 300 K of the bovine pancreatic trypsin inhibitor (BPTI), consisting of 454 heavy atoms, are compared: one of BPTI in vacuo, one of BPTI in a box with 2647 spherical nonpolar solvent atoms, and one of BPTI surrounded by fixed crystal image atoms. Both average and time-dependent molecular properties are examined to determine the effect of the environment on the behavior of the protein. The dynamics of BPTI in solution or in the crystal environment are found to be very similar to that found in the vacuum calculation. The primary difference in the average properties is that the equilibrium structure in the presence of solvent or the crystal field is significantly closer to the X-ray structure than is the vacuum result; concomitantly, the more realistic environment leads to a number density closer to experiment. The presence of solvent has a negligible effect on the overall magnitude of the positional or dihedral angle fluctuations in the interior of the protein; however, there are changes in the decay times of the fluctuations of interior atoms. For surface residues, both the magnitude and the time course of the motions are significantly altered by the solvent. There tends to be an increase in the displacements of long side chains and the flexible parts of the main chain that protrude into the solvent. Further, these motions tend to have a more diffusive character with longer relaxation times than in vacuo. The crystal environment has a specific effect on a number of side chains which are held in relatively fixed positions through hydrogen-bond and electric interactions with the neighboring protein atoms. Most of the effects of the solution environment seem to be sufficiently nonspecific that it may be possible to model them by applying a mean field and stochastic dynamic methods.

Animals↗
PubMed1982

Fluctuations and averaging of proton chemical shifts in the bovine pancreatic trypsin inhibitor.

The effects of motional averaging on the aromatic ring-current contribution to the proton chemical shifts in proteins are examined. Atomic trajectories obtained from a 96-ps molecular dynamics simulation of the bovine pancreatic trypsin inhibitor are used in conjunction with the Johnson-Bovey model of ring-current shifts to calculate the time evolution of the proton chemical shifts. Although large high-frequency fluctuations are observed (often greater than +/- 1 ppm), the average shift values in most cases are close to those obtained from the average structure; for some protons, significant differences are found. The calculated trends are used to probe the relationship between the average structure, atomic motions, and observed values of the proton chemical shifts. It is concluded that chemical shift values are in general most sensitive to the average structure of the protein and, because of the averaging involved, cannot be used directly to probe the short time structural fluctuations.

Animals↗
PubMed1982

Aplasia cutis congenita in two sibs discordant for pyloric atresia.

We report two sibs who were the products of a consanguineous mating, and who had an extensive form of aplasia cutis congenita (ACC). In one of them the generalized skin disorder was manifested by slipping off of the epidermis and mucous membranes with the slightest trauma. This sib also had pyloric atresia and other congenital malformations. Two hypotheses are presented to explain the discordance between the siblings for the abnormalities other than the ACC. One hypothesis assumes varying degrees of severity of the same autosomal recessive disease. The second suggests linkage between the gene for ACC and the gene for an epidermolysis bullosa (EB)-like disorder and pyloric atresia. a recombination event involving the EB-pyloric atresia gene in one carrier parent would then lead to an offspring with only ACC. Prenatal diagnosis is suggested by monitoring alpha-fetoprotein levels in aminotic fluid.

Abnormalities, Multiple↗
PubMed1982

Pharmacokinetic aspects of caffeine in premature infants with apnoea.

The pharmacokinetics of caffeine was examined in 13 premature infants (gestational age 25-34 weeks, birth weight 920-2060 g, postnatal age 1-42 days) who received the drug for treatment of apnoea. Caffeine (1% aqueous solution) was given i.v. in single doses: guided by the clinical response infants received between one and seven (mean 2.6) doses of 15 mg/kg. Mean (+/- SE; range) Clb was extremely slow - 8.5 ml/kg/h (+/- 0.4; 5.8-12.2), t1/2 was prolonged - 65.0 h (+/- 3.7; 48.2-87.5 h) and Vd was 0.781/kg(+/- 0.04; 0.47-1.01). No significant correlation was found between Clb, t1/2 and postnatal age in the whole group or in individual infants. Effective plasma concentrations varied over a wide range (12-36 micrograms/ml) and overlapped with subtherapeutic concentrations (less than or equal to 24 micrograms/ml). Single doses of 15 mg/kg i.v. or p.o. prevented apnoea in most cases, if necessary followed by additional doses. Monitoring the blood level of caffeine in infants receiving frequent repeated doses is necessary to prevent toxicity.

Apnea↗
PubMed1982

Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects.

The crystal structure and a 96-ps molecular dynamics simulation used to analyze structural and motional contributions to spin-lattice (T1) relaxation times of phenylalanine and tyrosine C gamma carbons of the pancreatic trypsin inhibitor. The H beta and H delta protons geminal to C gamma are calculated to account for approximately 80% of the dipolar relaxation for each residue. Experimental T1 values for the phenylalanine residues obtained at 25 MHz are observed to be 15-25% longer than estimates based on the rigid crystal structure. It is shown how an increase in T1 can be related to order parameters for the picosecond motional averaging of the important C,H dipolar interactions, and how these order parameters can be calculated from a protein molecular dynamics trajectory.

Animals↗
PubMed1982

Dynamical theory of activated processes in globular proteins.

A method is described for calculating the reaction rate in globular proteins of activated processes such as ligand binding or enzymatic catalysis. The method is based on the determination of the probability that the system is in the transition state and of the magnitude of the reactive flux for transition-state systems. An "umbrella sampling" simulation procedure is outlined for evaluating the transition-state probability. The reactive flux is obtained from an approach described previously for calculating the dynamics of transition-state trajectories. An application to the rotational isomerization of an aromatic ring in the bovine pancreatic trypsin inhibitor is presented. The results demonstrate the feasibility of calculating rate constants for reactions in proteins and point to the importance of solvent effects for reactions that occur near the protein surface.

Chemical Phenomena↗
PubMed1982

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior.

The mean square amplitudes of atomic fluctuations for a polypeptide (decaglycine) alpha-helix evaluated from molecular dynamics simulations at seven temperatures between 5 and 300 K are compared with analytic harmonic results and with experimental values. Above 100 K the harmonic approximation significantly underestimates the amplitudes of the displacements. Analysis of the time dependence of the fluctuations shows that low-frequency modes (<75 cm(-1)) dominate the atomic fluctuations and that there is a contribution with a very long relaxation time (>10 ps). Quantum corrections to the amplitude of the fluctuations are found to be small above 50 K. The mean square amplitudes obtained from the molecular dynamics simulations are compared with the values derived from x-ray temperature (Debye-Waller) factors for metmyoglobin (80, 250, and 300 K) and ferrocytochrome c (300 K).

Journal Article↗