Binding conformers searching method for ligands according to the structures of their receptors and its application to thrombin inhibitors. (9/8682)

AIM: To develop a method of finding binding conformers for ligands according to the three-dimensional structures of their receptors. METHODS: Combining the systematic search method of ligand with the molecular docking approach of ligand fitting into its receptor, we developed a binding conformer searching method for ligands. RESULTS: The binding conformers of phosphonopeptidyl thrombin inhibitors were recognized. The binding (interaction) energies between these inhibitors and thrombin were calculated with molecular mechanical method. CONCLUSION: Both of the total binding energies and steric binding energies have good correlations with the inhibitory activities of these thrombin inhibitors, demonstrating that our approach is reasonable. It can also be used to explain the inhibition mechanism of thrombin interacting with these inhibitors.  (+info)

Hydrocarbon chain packing and the effect of ethanol on the thermotropic phase behavior of mixed-chain phosphatidylglycerols. (10/8682)

Previous studies in this laboratory have delineated the relationship between the acyl chain asymmetry of mixed-chain phosphatidylcholines and the effect of ethanol concentration ([EtOH]) on their melting behavior (Li et al., Biophys J., 70 (1996) 2784-2794). This present investigation extends these findings to another phospholipid family by using high-resolution differential scanning calorimetry (DSC) to characterize the effect of ethanol concentration on the main phase transition temperature (Tm) of five molecular species of mixed-chain phosphatidylglycerol (PG). For C(14):C(18)PG, C(15):C(17)PG, C(16):C(16)PG, and C(17):C(15)PG, a biphasic profile in the Tm versus [EtOH] plot was observed, and the minimum in the plot for each PG occurred at 33, 15, 19, and 36 mg/ml, respectively. This biphasic behavior is typical of phospholipids whose acyl chain asymmetry is fairly small. For C(18):C(14)PG, only a linear decrease in the Tm was observed as a function of ethanol concentration; this effect is characteristic of highly asymmetric phospholipids. Our DSC results obtained with mixed-chain PG in the presence of ethanol demonstrate that the acyl chain asymmetry of the five lipids studied can be ranked as follows: C(15):C(17)PG+info)

Thermotropic phase behavior of mixed-chain phosphatidylglycerols: implications for acyl chain packing in fully hydrated bilayers. (11/8682)

In this communication we report the first systematic investigation of the thermodynamic properties of fully hydrated mixed-chain phosphatidylglycerols (PG) using high-resolution differential scanning calorimetry (DSC). The crystal structure of dimyristoylphosphatidylglycerol shows an acyl chain conformation that is nearly opposite to that of phosphatidylcholine (PC). In PC, the sn-1 chain is straight while the sn-2 chain contains a bend; for PG, the sn-1 contains a bend while the sn-2 chain is in the all-trans conformation (R.H. Pearson, I. Pascher, The molecular structure of lecithin dihydrate, Nature, 281 (1978) 499-501; I. Pascher, S. Sundell, K. Harlos, H. Eibl, Conformational and packing properties of membrane lipids: the crystal structure of sodium dimyristoylphosphatidylglycerol, Biochim. Biophys. Acta, 896 (1987) 77-88). If the structure of PG found in the single crystal can be extrapolated to that in the fully hydrated gel-state bilayer, the observed difference in acyl chain conformations implies that modulation of the acyl chain asymmetry will have an opposite effect on the thermotropic phase behavior of PG and PC. For example, it is expected, based on the crystal structures, that C(15):C(13)PG should have a higher main phase transition temperature (Tm) than C(14):C(14)PG, and C(13):C(15)PG should have a lower Tm than C(14):C(14)PG. However, our DSC studies show clearly that the expectation is not borne out by experimental data. Rather, the Tm values of C(15):C(13)PG, C(14):C(14)PG, and C(13):C(15)PG are 18.2 degrees C, 23.1 degrees C, and 24.4 degrees C, respectively. Several other PGs, each with a unique acyl chain composition, have also been studied in this laboratory using high-resolution DSC. It is shown that the acyl chain conformation of fully hydrated PG in general is nearly opposite to that seen in the PG crystal structure.  (+info)

Nonenzymatic reduction of benzo(a)pyrene diol-epoxides to trihydroxypentahydrobenzo(a)pyrenes by reduced nicotinamide adenine dinucleotide phosphate. (12/8682)

The diol-epoxide r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene is a potent mutagen and possibly the ultimate carcinogenic form of benzo(a)pyrene. A (7/8,9)-trihydroxy-7,8,9,10,10-pentahydrobenzo(a)pyrene is formed from the diol-epoxide r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydroxybenzo(a)pyrene by reduction with reduced nicotinamide adenine dinucleotide phosphate. Its formation is linear with reduced nicotinamide adenine dinucleotide phosphate concentration and does not require the presence of enzyme. A (7,9/8)-trihydroxy-7,8,9,10,10-pentahydrobenzo(a)pyrene is similarly formed from the diol-epoxide r-7,t-8-dihydroxy-c-9,10-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene by reduction with reduced nicotinamide adenine dinucleotide phosphate. The structures of the trihydroxypentahydrobenzo(a)pyrenes were established by their ultraviolet absorption and mass spectra and their reaction with potassium triacetylosmate.  (+info)

Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine. (13/8682)

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2',5')adenosine is reported at 2.06 A resolution. The refined model has a crystallographic R-factor of 0.184 and good stereochemistry. The quality of the electron density maps enables the structure of both the inhibitor and active site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts an extended conformation with the pyrimidine and purine base interacting with Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His119, and Phe120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specific water molecules believed to be relevant to catalytic activity. Upon binding of the dinucleotide, small but significant modifications of the tertiary and quaternary structure of the protein are observed. The ensuing correlation of these modifications with the catalytic activity of the enzyme is discussed.  (+info)

Analysis of zinc binding sites in protein crystal structures. (14/8682)

The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.  (+info)

Molecular mechanisms of resistance: free energy calculations of mutation effects on inhibitor binding to HIV-1 protease. (15/8682)

The changes in the inhibitor binding constants due to the mutation of isoleucine to valine at position 84 of HIV-1 protease are calculated using molecular dynamics simulations. The calculations are done for three potent inhibitors--KNI-272, L-735,524 (indinavir or MK-639), and Ro 31-8959 (saquinavir). The calculations agree with the experimental data both in terms of an overall trend and in the magnitude of the resulting free energy change. HIV-1 protease is a homodimer, so each mutation causes two changes in the enzyme. The decrease in the binding free energy from each mutated side chain differs among the three inhibitors and correlates well with the size of the cavities induced in the protein interior near the mutated residue. The cavities are created as a result of a mutation to a smaller side chain, but the cavities are less than would be predicted from the wild-type structures, indicating that there is significant relaxation to partially fill the cavities.  (+info)

cAMP-dependent phosphorylation of the tetrodotoxin-resistant voltage-dependent sodium channel SNS. (16/8682)

1. Protein kinase A (PKA) modulation of tetrodotoxin-resistant (TTX-r) voltage-gated sodium channels may underly the hyperalgesic responses of mammalian sensory neurones. We have therefore examined PKA phosphorylation of the cloned alpha-subunit of the rat sensory neurone-specific TTX-r channel SNS. Phosphorylation of SNS was compared with that of a mutant channel, SNS(SA), in which all five PKA consensus sites (RXXS) within the intracellular I-II loop had been eliminated by site-directed mutagenesis (serine to alanine). 2. In vitro PKA phosphorylation and tryptic peptide mapping of SNS and mutant SNS(SA) I-II loops expressed as glutathione-S-transferase (GST) fusion proteins confirmed that the five mutated serines were the major PKA substrates within the SNS I-II loop. 3. SNS and SNS(SA) channels were transiently expressed in COS-7 cells and their electrophysiological properties compared. In wild-type SNS channels, forskolin and 8-bromo cAMP produced effects consistent with PKA phosphorylation. Mutant SNS(SA) currents, however, were not significantly affected by either agent. Thus, elimination of the I-II loop PKA consensus sites caused a marked reduction in PKA modulation of wild-type channels. 4. Under control conditions, the voltage dependence of activation of SNS(SA) current was shifted to depolarized potentials compared with SNS. This was associated with a slowing of SNS(SA) current inactivation at hyperpolarized potentials and suggested a tonic PKA phosphorylation of wild-type channels under basal conditions.5. We conclude that the major substrates involved in functional PKA modulation of the SNS channel are located within the intracellular I-II loop.  (+info)