Biomedical subjects

C L Brooks

Publications and source records attributed to C L Brooks.

At least 19 recordsLinked to original sources

PubMed1992

Stability of a model beta-sheet in water.

We have used molecular dynamics simulations to determine the stability in water of a model beta-sheet formed by two alanine dipeptide molecules with two intermolecular hydrogen bonds in the closely spaced antiparallel arrangement. In this paper we describe our computations of the binding free energy of the model sheet and a portion of the free energy surface as a function of a reaction co-ordinate for sheet formation. We used the free energy surface to identify stable conformations along the reaction co-ordinate. To determine whether or not the model sheet with two hydrogen bonds is more stable than a single amide hydrogen bond in water, we compared the results of the present calculations to results from our earlier study of linear hydrogen bond formation between two formamide molecules (the formamide "dimer"). The free energy surfaces for the sheet and formamide dimer each have two minima corresponding to locally stable hydrogen-bonded and solvent-separated configurations. The binding free energies of the model sheet and the formamide dimer are -5.5 and -0.34 kcal/mol, respectively. Thus, the model sheet with two hydrogen bonds is quite stable while the simple amide hydrogen bond is only marginally stable. To understand the relative stabilities of the model sheet and formamide dimer in terms of solute-solute and solute-water interactions, we decomposed the free energy differences between hydrogen-bonded and solvent-separated conformations into energetic and entropic contributions. The changes in the peptide-peptide energy and the entropy are roughly twice as large for the sheet as they are for the formamide dimer. The magnitude of the peptide-water energy difference for the sheet is less than twice (by about 3.5 kcal/mol) that for the formamide dimer, and this accounts for the stability of the sheet. The presence of the side-chains and/or blocking groups apparently prevents the amide groups in the sheet from being solvated as favorably in the separated arrangement as in the formamide dimer, where the amide groups are completely exposed to the solvent.

Alanine↗

PubMed1992

Characterization of "native" apomyoglobin by molecular dynamics simulation.

We have used molecular dynamics simulation methods to study the structure and fluctuations of "native" apomyoglobin in aqueous solution for a period of greater than 0.5 nanosecond. This work was motivated by the recent attempts of Hughson et al. to characterize the structure and motion of both this molecule and the less compact, acid stabilized I stage, using methods of pulsed H/2H exchange. The study of these systems provides new insights into protein folding intermediates and our simulation has yielded a detailed model for structure and fluctuations in apomyoglobin which complements the experimental studies. We find that local (short-time) fluctuations agree well with fluctuations observed for the holoprotein in aqueous solution, as well as results from the crystallographic B-factors. In addition, the structural features we observe for native apomyoglobin are very similar to the holoprotein, in basic agreement with the findings of Hughson et al. By examining larger-scale motions, developing only over timescales in excess of a 100 picoseconds, we are able to identify conformationally "labile" and "non-labile" regions within native apomyoglobin. These regions correspond extremely well to those identified in the nuclear magnetic resonance experiments as unstable and stable "folding subdomains" in the I state of apomyoglobin. Overall we find that helices A, B, E, G and H show the least amount of motion and helices C, D and F move substantially over the timescales examined. The major motions, and the primary difference between the holo and apo structures as we have observed them, are due to the shifting motion of helices C, D and F into the vacant heme cavity. We also find that motions at the interface of helical segments can be large, with one important exception being the chain segment connecting helices G and H. This segment of chain interacts with the conformationally "non-labile" helix A to form a relatively rigid subdomain composed of helices A, G and H. We believe that these findings provide direct support for the suggestion of Hughson et al. that helices A, G and H constitute a compact subdomain that remains in a native-like conformation as the protein begins to unfold in environments of decreasing pH.

Apoproteins↗

PubMed1992

Casein, actin, and tubulin expression during early involution in bovine and murine mammary tissue.

Hybridization methods and in vitro translation were used to examine the expression and functional condition of messenger RNA encoding caseins and cytoskeletal proteins in the mammary gland during early involution. In the mouse, steady state mRNA levels for alpha-, beta-, and gamma-caseins coordinately decreased to 20% of initial levels between 12 and 72 h after pup removal. In vitro translatability of mouse casein mRNA, as determined by immunoprecipitation, electrophoresis, and gel slice counting, revealed a pattern that closely paralleled mRNA expression. In contrast, bovine casein mRNA levels were only slightly reduced by 72 h postmilking, whereas in vitro translatability decreased by about one-half. Northern blot analysis of total mouse mammary RNA that were hybridized with probes to cytoskeletal proteins showed a gradual decrease of alpha-tubulin mRNA, but an increase in beta-actin mRNA during early involution. Two-dimensional gel analysis of in vitro translated products indicated a concordant increase in beta-gamma-actin. In the cow, beta-actin mRNA at 72 h of involution was equal to or greater than that during lactation. These results demonstrate the generally slower involution response in the cow and suggest that differing regulations are involved. Early events of cellular involution may be related to a reorganization of the cytoskeleton.

Actins↗

PubMed1991

Nanosecond time scale folding dynamics of a pentapeptide in water.

Reverse turns, four-residue sections of polypeptides where the chain changes direction by about 180 degrees, are thought to be important protein folding initiation structures. However, the time scale and mechanism for their formation have yet to be determined experimentally. To develop a microscopic picture of the formation of protein folding initiation structures, we have carried out a pair of 2.2-ns molecular dynamics simulations of Tyr-Pro-Gly-Asp-Val, a peptide which is known to form a high population of reverse turns in water. In the first simulation, which was started with the peptide in an ideal type II reverse turn involving the first four residues, the turn unfolded after about 1.4 ns. After about 0.6 ns in the second simulation, which was started with the peptide in a fully extended conformation, the peptide folded into a type II turn which had a transient existence before unfolding. The peptide remained unfolded for another 0.9 ns before folding into a type I turn involving the last four residues. The type I turn lasted for about 0.2 ns before unfolding. Thus, these simulations showed that protein folding initiation structures can form and dissolve on the nanosecond time scale. Furthermore, the atomic-level detail of the simulations allowed us to identify some of the interactions which can stabilize the folded structures. The type II turns were stabilized by either a salt bridge between the terminal groups or a backbone-C-terminal group hydrogen bond, and the type I turns were stabilized by a hydrophobic interaction between the proline and valine-side chains.

Amino Acid Sequence↗

PubMed1991

Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides.

We used molecular dynamics simulations to study the folding/unfolding of one of turn of an alpha helix in Ac-(Ala)3-NHMe and Ac-(Val)3-NHMe. Using specialized sampling techniques, we computed free energy surfaces as functions of a conformational coordinate that corresponds to alpha helices at small values and to extended conformations at large values. Analysis of the peptide conformations populated during the simulations showed that alpha helices, reverse turns, and extended conformations correspond to minima on the free energy surfaces of both peptides. The free energy difference between alpha helix and extended conformations, determined from the equilibrium constants for helix unfolding, is approximately -1 kcal/mol for Ac-(Ala)3-NHMe and -5 kcal/mol for Ac-(Val)3-NHMe. The mechanism observed in our simulations, which includes reverse turns as important intermediates along the helix folding/unfolding pathway, is consistent with a mechanism proposed previously. Our results predict that both peptides (but especially the Ala peptide) have a much larger equilibrium constant for helix initiation than is predicted by the helix-coil transition theory with the host-guest parameters. We also predict a much greater difference in the equilibrium constants than the theory predicts. Insofar as helix initiation is concerned, our results suggest that the large difference between the helical propensities of Ala and Val cannot be explained by simple concepts such as side-chain rotamer restriction or unfavorable steric interactions. Rather, the origin of the difference appears to be quite complicated because it involves subtle differences in the solvation of the two peptides. The two peptides have similar turn-extended equilibria but very different helix-turn equilibria, and the difference in helical propensities reflects the fact that the helix-turn equilibrium strongly favors the turns in Ac-(Val)3-NHMe, while it favors the helices in Ac-(Ala)3-NHMe. We also computed thermodynamic decompositions of the free energy surfaces, and these revealed that the helix-turn equilibria are vastly different primarily because the changes in peptide-water interactions that accompany helix-to-turn conformational changes are qualitatively different for the two peptides.

Alanine↗

PubMed1991

Virtual rigid body dynamics.

An important direction in biological simulations is the development of methods that permit the study of larger systems and/or longer simulation time scales than is currently feasible by molecular dynamics. One such method designed with this objective in mind is stochastic boundary molecular dynamics (SBMD). SBMD was developed for the characterization of spatially localized processes in proteins, and has been shown to successfully reproduce structural and dynamical properties of these macromolecules, as compared to a molecular dynamics control simulation, when concerted or global motions are not present. The virtual rigid body dynamics method presented in this work extends the range of applicability of the SBMD method, by providing a framework to include these important long time scale conformational transitions. In this paper we describe the two-step implementation of the virtual rigid body model: first, the reduction of the full atomic representation to a reduced particle (virtual bond) model, and second, the propagation of the dynamics of flexibly connected rigid bodies containing virtual atom sites.

Biopolymers↗

PubMed1991

A CHARMM analysis of the conformations of the metastasis-inhibiting laminin pentapeptide.

The metastatic invasion of basement membrane by tumor cells involves the binding of tumor cells to laminin. Laminin, a glycoprotein, is a major component of basement membrane. Both tumor and normal cells express a high-affinity receptor for laminin; however, the expression is more pronounced with tumor cells. The pentapeptide, Tyr-Ile-Gly-Ser-Arg, (YIGSR), an amino acid sequence from the B1 chain of laminin, was found to compete with laminin for binding to the laminin receptor. The binding of tumor cells to laminin can be inhibited competitively by YIGSR and, in mice, this has been shown to be translated into a reduction in metastasis. Reports of structural modifications of YIGSR leading to molecules with enhanced activity led us to attempt to learn more about the secondary structure of YIGSR. Through the use of CHARMM, a molecular mechanics program, we were able to discover a conformation of N-acetyl-YIGSR-NHCH3 that is stable over a wide range of dielectric constants. In this conformation the arginine side chain acts to hold Tyr, Ile, and Gly in a partial right-handed alpha helix. We speculate that this partial alpha helical structure is necessary for binding to the lamin receptor and thereby its antimetastatic activity.

Amino Acid Sequence↗

PubMed1991

Essential role of urease in pathogenesis of gastritis induced by Helicobacter pylori in gnotobiotic piglets.

A mutant strain of Helicobacter pylori with weak urease activity was created by using N-methyl-N'-nitro-N-nitrosoguanidine. The urease activity of the mutant (0.036 +/- 0.009 nmol of urea per micrograms of bacterial protein per min) was 0.4% of that of the parental strain (8.20 +/- 2.30 nmol of urea per micrograms of bacterial protein per min). The mutant was otherwise indistinguishable from the parental strain. Both demonstrated prominent catalase and oxidase activities, and both produced vacuolating cytotoxin. Restriction endonuclease and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns and ultrastructure were identical for the two strains. The mutant was fully motile, as evaluated by spreading in soft agar and by direct microscopic examination. Growth rate and colony size and morphology were identical for the mutant and parental strains. Seventeen gnotobiotic piglets were challenged with either the mutant or the parental strain and sacrificed 3 or 21 days after challenge. Gastric tissue was examined histologically and cultured for H. pylori. Of seven piglets challenged with the parental strain, all became infected. H. pylori was not recovered from any of 10 piglets challenged with the urease-negative strain. Lymphofollicular gastritis was present in all seven piglets challenged with the parental strain but in none of the piglets challenged with the urease-negative strain. These results suggest that prominent urease activity is essential for colonization by H. pylori.

Animals↗

PubMed1990

Reverse turns in blocked dipeptides are intrinsically unstable in water.

We have carried out molecular dynamics simulations to study the conformational equilibria of two blocked dipeptides, Ac-Ala-Ala-NHMe and trans-Ac-Pro-Ala-NHMe, in water (Ac, amino-terminal blocking group COCH3; NHMe, carboxy-terminal blocking group NHCH3). Using specialized sampling techniques we computed free-energy surfaces as functions of a conformation co-ordinate that corresponds to hydrogen-bonded reverse turns at small values and to extended conformations at large values. The free-energy difference between hydrogen-bonded reverse turn conformations and extended conformations, determined from the equilibrium constants for reverse turn unfolding, is approximately -5 kcal/mole for Ac-Ala-Ala-NHMe, and -10 kcal/mole for Ac-Pro-Ala-NHMe. These results demonstrate that reverse turns in blocked dipeptides are intrinsically unstable in water. That is, in the absence of strongly stabilizing sequence-specific inter-residue interactions involving side-chains and/or charged terminal groups, the extended conformations of small peptides are highly favored in solution. By thermodynamically decomposing the free-energy differences, we found that the peptide-water entropy is the primary reason for the exceptional stability of the extended conformations of both peptides, and that the differences between the two peptides are primarily due to differences in the peptide-water interactions. In addition, we assessed the "proline effect" on the conformational equilibria by comparing the differences in configurational entropies between the reverse turn and extended conformations of the two peptides. As expected, the extended conformation of the Pro-Ala peptide is destabilized by reduced configurational entropy, but the effect is negligible in the blocked dipeptides. Finally, we compared our results with the results of several other experimental studies to identify some of the specific interactions that may be responsible for stabilizing reverse turns in small peptides in solution.

Amino Acid Sequence↗

PubMed1990

Phosphorylated variant of bovine prolactin.

Bovine pituitary explants and cell cultures were incubated with [32P]orthophosphate. Extracts were prepared from the explants and analyzed by sodium dodecyl sulfate-containing acrylamide gel electrophoresis and autoradiography revealing a phosphoprotein that co-migrated with authentic bovine prolactin. Clonal antibodies to bovine prolactin were produced, purified and used to prepare affinity columns. Extracts of [32P]orthophosphate-labeled explants and cells or media were applied to prolactin affinity columns and a radiolabeled protein was eluted with a pH 2.8 wash. The eluted protein was identified as prolactin by co-migration with standard on gel electrophoresis and by amino acid analysis. Treatment of immunoaffinity-purified pituitary prolactin with alkaline phosphatase reduced the phosphate associated with prolactin in a time-dependent manner, indicating a covalent phosphate linkage. Autoradiography of gels revealed prolactin from explants, cells and their associated media to be a phosphoprotein. A phosphorylated variant of bovine prolactin is synthesized and secreted in both explant and cell cultures.

Animals↗

PubMed1990

The solution conformations of ferrichrome and deferriferrichrome determined by 1H-NMR spectroscopy and computational modeling.

We have applied computational procedures that utilize nmr data to model the solution conformation of ferrichrome, a rigid microbial iron transport cyclohexapeptide of known x-ray crystallographic structure [D. van der Helm et al. (1980) J. Am. Chem. Soc. 102, 4224-4231]. The Al3+ and Ga3+ diamagnetic analogues, alumichrome and gallichrome, dissolved in d6-dimethylsulfoxide (d6-DMSO), were investigated via one- and two-dimensional 1H-nmr spectroscopy at 300, 600, and 620 MHz. Interproton distance constraints derived from proton Overhauser experiments were input to a distance geometry algorithm [T. F. Havel and K. Wüthrich (1984) Bull. Math. Biol. 46, 673-691] in order to generate a family of ferrichrome structures consistent with the experimental data. These models were subsequently optimized through restrained molecular dynamics/energy minimization [B. R. Brooks et al. (1983) J. Comp. Chem. 4, 187-217]. The resulting structures were characterized in terms of relative energies and conformational properties. Computations based on integration of the generalized Bloch equations for the complete molecule, which include the 14N-1H dipolar interaction, demonstrate that the x-ray coordinates reproduce the experimental nuclear Overhauser effect time courses very well, and indicate that there are no significant differences between the crystalline and solution conformations of ferrichrome. A similar study of the metal free peptide, deferriferrichrome, suggests that at least two conformers are present in d6-DMSO at 23 degrees C. Both are different from the ferrichrome structure and explain, through conformational averaging, the observed amide NH and CH alpha multiplet splittings. The occurrence of interconverting peptide backbone conformations yields an increased number of sequential NH-CH alpha and NH-NH Overhauser connectivities, which reflects the mean value of r-6 dependence of the dipolar interaction. Our results support the idea that, in the case of structurally rigid peptides, moderately accurate distance constraints define a conformational subspace encompassing the "true" structure, and that energy considerations reduce the size of this subspace. For flexible peptides, however, the straight-forward approach can be misleading since the nmr parameters are averaged over substantially different conformational states.

Amino Acid Sequence↗

PubMed1990

Protein-drug interactions: characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives.

Structural and thermodynamic interactions for the binding of trimethoprim and related congeners to the binary complex of dihydrofolate reductase (from chicken) and NADPH are explored using free energy simulation methods. Good agreement between structures from experimental X-ray refinement and molecular dynamics simulations is found for the complexes. Agreement with thermodynamic measurements is found as well. Our thermodynamic calculations suggest that entropic contributions and desolvation thermodynamics can play a crucial role in overall binding, and that extreme care must be taken in the use of simple model building to rationalize or predict protein-drug binding.

Animals↗

PubMed1990

The effect of placenta on lactogen receptor in pseudopregnant rabbits.

This study examines the effect of placenta on the evolution of lactogen receptor in virgin pseudopregnant rabbit ovary, adrenal gland and mammary gland. Pseudopregnancy was induced with human chorionic gonadotropin. Does were injected with vehicle or placenta daily beginning on day six of the pseudopregnancy. Vehicle-treated rabbits during pseudopregnancy demonstrated a peak of ovarian lactogen receptor on day eight of pseudopregnancy. After treatment with placental homogenate a shift of this peak to twenty days of pseudopregnancy occurred. Lactogen receptor in adrenal and mammary gland membranes had peak receptor concentrations on day 14 of pseudopregnancy. Injection of placenta induced a shift to day 17 and days 17-20 in mammary and adrenal membranes, respectively. Serum concentrations of progesterone, estradiol, 20 alpha dihydroprogesterone and prolactin in placenta-treated groups were not significantly different from those of vehicle-treated groups. Treatment of pseudopregnant does with a composite of hormones at the concentrations found in placental homogenate produced no modulation of tissue lactogen receptor. Fractionation of 20-day pregnant rabbit placenta revealed that 80% of this activity could be found in the acetone extract while 20% was in the bicarbonate extract. These observations suggest that increases of lactogen receptor in ovary, adrenal and mammary glands occur during pseudopregnancy in rabbits and it is further concluded that placenta can alter these receptor induction patterns to ones similar to those seen in these tissues during pregnancy.

Adrenal Glands↗

PubMed1990

Failure of pH to predict ionized calcium percentage in healthy horses.

Blood, serum, and plasma total calcium concentrations and plasma and serum ionized calcium concentrations were anaerobically determined by use of a calcium-specific electrode for samples obtained from 39 healthy horses. Mean (+/- SD) serum ionized calcium concentration was 6.6 +/- 0.3 mg/dl (1.6 +/- 0.1 mmol/L) and the mean serum ionized calcium percentage was 58.2 +/- 3.4%. Serum ionized calcium percentage was not significantly correlated with serum pH. Plasma ionized calcium percentage was weakly correlated with plasma pH (r = -0.480; P less than or equal to 0.05). Ionized calcium concentration was determined in serum samples manipulated in vitro by additions of 1 to 80 microliters of 0.1N hydrochloric acid or sodium hydroxide to yield 6 to 10 pH values between 6.8 and 8.2. In all horses, the relationship between serum ionized calcium percentage and serum pH at these pH values was then examined by use of a repeated-measures multiple regression analysis. Correlations between serum ionized calcium percentage and adjusted serum pH value for each horse were highly significant (P less than or equal to 0.05); however, analysis of pooled data from all horses indicated that a statistically significant relationship between serum pH and ionized calcium percentage did not exist. Lack of a significant relationship between these variables was most likely attributable to heterogeneity of variance of ionized calcium percentage among horses, reflecting variation in undefined biochemical constituents of serum that affect the equilibrium of calcium binding. When it is essential to evaluate the calcium status of a horse, direct measurement of serum ionized calcium concentration is recommended.

Analysis of Variance↗

PubMed1989

Thermodynamics of amide hydrogen bond formation in polar and apolar solvents.

We present the initial findings of a theoretical study of hydrogen bond formation between two formamide molecules in water and in carbon tetrachloride. These systems were chosen as the simplest models for secondary structure formation in the polar environment near the protein surface and the apolar environment of the protein interior. We have employed thermodynamic simulation methods to obtain absolute binding free energies and free energy profiles for the formation of peptide hydrogen bonds in the two solvents. We find that the amide hydrogen bond is stable by 8.4 kcal/mol in CCl4, and by 0.3 kcal/mol in water. Our results indicate also that the hydrogen-bonded dimer is 2.2 kcal/mol more stable in water than it is in CCl4. We compare our results with those from experiment, and discuss their use in interpreting mechanisms of protein folding.

Acetamides↗

PubMed1989

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme.

The stochastic boundary molecular dynamics methodology is applied to the active site of the enzyme lysozyme. A comparison is made of in vacuo dynamics results from the stochastic boundary method and a full conventional molecular dynamics simulation of lysozyme. Excellent agreement between the two approaches is obtained. The influence of solvent on the residues in the active site region is explored and it is shown that both the structure and dynamics are affected. Of particular importance for the structure of the protein is the solvation of polar residues and the stabilization of like-charged ion pairs. The magnitude of the fluctuations is only slightly altered by the solvent; the overall increase in the root-mean-square fluctuations, relative to the vacuum run, is 11%. The solvent effect on dynamical properties is found not to be simply related to the solvent viscosity. Both the solvent exposure and dynamic aspects of protein-solvent interactions, including the relative time scales of the motions, are shown to play a role. The effects of the protein on solvent dynamics and structure are also observed to be significant. The solvent molecules around atoms in charged, polar and apolar side-chains show markedly different diffusion coefficients as well as exhibiting different solvation structures. One key example is the water around apolar groups, which is much less mobile than bulk water, or water solvating polar groups.

Animals↗

PubMed1989

Two physiological substrate-specific casein kinases are present in the bovine mammary gland.

Two species of casein kinase from lactating bovine mammary gland have been identified; a Ca2+- and CM-independent casein kinase and a Ca2+- and CM-dependent casein kinase. The Ca2+- and CM-independent casein kinase phosphorylates previously dephosphorylated alpha s1-, beta- or kappa-casein while the Ca2+- and CM-dependent casein kinase prefers previously dephosphorylated beta- or kappa-casein as substrates. Two activities are indicated by their substrate specificity, sensitivity to Ca2+ and CM, pH maxima, and differential solubilization by anionic detergents. The presence of a regulated casein kinase in the lactating mammary gland suggests that casein phosphorylation may be a regulator of micelle formation or secretion.

Animals↗

PubMed1989

Separation of parathyroid hormone-like activity from transforming growth factor-alpha and -beta in the canine adenocarcinoma (CAC-8) model of humoral hypercalcemia of malignancy.

A canine adenocarcinoma model (CAC-8) of humoral hypercalcemia of malignancy was evaluated for transforming growth factors (TGF)-alpha and -beta, PTH-like activity [adenylate cyclase-stimulating activity (ACSA)], and in vitro bone-resorbing activity. Biological activities present in CAC-8 were separated by reverse phase or cation exchange HPLC. TGF alpha in tumor extract was separated from TGF beta and ACSA by reverse phase HPLC. TGF alpha eluted between 26-30% acetonitrile and was identified by RIA. After the initial reverse phase separation, TGF beta and ACSA in tumor extract coeluted between 36-38% acetonitrile. Sequential cation exchange followed by reverse phase HPLC separated TGF beta from ACSA. Evaluation of fractions containing ACSA using an in vitro bone-resorbing assay demonstrated copurification of ACSA and bone-resorbing activity. The PTH receptor antagonist [Nle8,18,Tyr34]bovine PTH-(3-34)-amide, but not [Nle8,18,Tyr34]bovine PTH-(7-34)-amide, completely inhibited ACSA in column eluates. Conditioned cell culture medium from CAC-8 primary cultures contained predominantly latent TGF beta that could be activated by acidification. These findings indicate that the CAC-8 model of cancer-associated hypercalcemia produces a PTH-like factor, TGF alpha, and TGF beta that were separable by reverse phase or cation exchange HPLC. This feature should be useful to investigate the role of TGFs and PTH-like proteins in the pathogenesis of humoral hypercalcemia of malignancy.

Adenocarcinoma↗