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At least 127 records · Page 7Linked to original sources
PubMed1994

Localization of two protease-sensitive regions separating distinct domains in the reovirus cell-attachment protein sigma 1.

Electron microscopy and sequence analysis have suggested the presence of distinct morphological regions within the reovirus cell attachment protein sigma 1. Kinking of purified sigma 1 observed by electron microscopy and sequence-predicted flexibility profiles suggest the presence of potential flexible regions in the molecule, most notably near the N-terminus, in the neck region and near the middle of the fiber. We have mapped the trypsin and chymotrypsin cleavage sites in sigma 1 by direct amino acid sequencing of gel-purified, proteolytic fragments of purified baculovirus-expressed sigma 1. The results indicated that both proteases cleave sigma 1 several times in one, or both, of two specific regions in the molecule. Further analysis using proteases with different cleavage specificities revealed the same general digestion pattern. The two protease-sensitive regions of sigma 1 were localized to the proposed N-terminal hinge region separating the hydrophobic anchor from the coiled-coil and to the C-proximal portion of the neck separating most of the fibrous tail from the globular head. The protease susceptibility of these regions indicates an open, accessible conformation supporting the notion of flexible regions that may be important in sigma 1 function.

Amino Acid Sequence↗
PubMed1985

Hypertriglyceridemia: lipoprotein receptors and atherosclerosis.

We have shown first, that apoB mediates the binding of small VLDL Sf 20-60 and IDL, as well as LDL, to the LDL receptor. Second, apoE of an appropriate, accessible conformation is required for the binding of large VLDL to the LDL receptor; HTG-VLDL Sf greater than 60 but not normal VLDL Sf greater than 60 have this apoE population. Third, the same population of apoE that mediates binding of HTG-VLDL Sf greater than 60 to the LDL receptor modulates its binding to the beta-VLDL receptor, but it is not required for the latter interaction. Fourth, a domain of processed apoB or apoB-48 in association with a domain of the inaccessible apoE is required for binding to and uptake by the beta-VLDL receptor. Fifth, our observations suggest that the abnormal catabolism of VLDL that occurs in hypertriglyceridemia may be explained by the abnormal uptake of HTG-VLDL by either the LDL or the beta-VLDL receptor pathway. Finally, we suggest that plasma proteases may route apoB/E-containing lipoproteins to macrophages for disposal, and this results in foam cell formation.

Apolipoproteins B↗
PubMed1993

Kinetic and physical characterization of force generation in muscle: a laser temperature-jump and length-jump study on activated and contracting rigor fibers.

Experiments are presented that probe the mechanism of contraction in normal activated muscle fibers and in heated rigor fibers. In activated fibers we subdivide the partial recovery of isometric tension during the Huxley-Simmons phase 2 into temperature-independent and temperature-dependent steps termed, respectively, phase 2fast and phase 2slow. Evidence is presented to show that phase 2fast arises from the perturbation of a damped elastic element in the cross-bridge and that phase 2slow is the manifestation of an endothermic, order-disorder transition responsible for de novo tension generation. These responses are common to both frog and rabbit fibers. The only difference between animals is that the kinetics of phase 2slow appears to scale with the working temperature of the muscle and not absolute temperature. Rigor fibers heated above the working temperature of the muscle contract. Tension generation is, as with activated fibers, endothermic. Tension transients following a laser temperature-jump of activated and heated rigor fibers are virtually indistinguishable on the basis of either the form or magnitude of the response. In length-jump experiments, tension recovery by heated rigor fibers consists of three exponentials with a tension-dependent rate for the medium speed step. Preliminary data indicate that the rigor cross-bridge operates over a distance of between 13.5 and 18 nm. Collectively, these data imply that tension generation in muscle arises from accessible conformational states in the proteins of the cross-bridge alone. ATP hydrolysis in active fibers and the heating of rigor fibers simply serve to shift these intrinsic conformational equilibria towards tension generation.

Animals↗
PubMed1996

The mitochondrial processing peptidase: function and specificity.

Targeting signals of mitochondrial precursors are cleaved in the matrix during or after import by the mitochondrial processing peptidase (MPP). This enzyme consists of two nonidentical alpha- and beta-subunits each of molecular weight of about 50 kDa. In mammals and fungi, MPP is soluble in the matrix, whereas in plants the enzyme is part of the cytochrome bc1 complex. MPP is a metalloendopeptidase which has been classified as a member of the pitrilysin family on the basis of the HXXEHX76E zinc-binding motif present in beta-MPP. Both subunits of MPP are required for processing activity. The alpha-subunit of MPP, which probably recognizes a three-dimensional motif adopted by the presequence, presents the presequence to beta-MPP, which carries the catalytic active site. MPP acts as an endoprotease on chemically synthesized peptides corresponding to mitochondrial presequences. Matrix-targeting signals and MPP cleavage signals seem to be distinct, although the two signals may overlap within a given presequence. The structural element helix-turn-helix, that cleavable presequences adopt in a membrane mimetic environment, may be required for processing but is not sufficient for proteolysis. Binding of the presequence by alpha-MPP tolerates a high degree of mutations of the presequence. alpha-MPP may present a degenerated cleavage site motif to beta-MPP in an accessible conformation for processing. The conformation of mitochondrial presequences bound to MPP remains largely unknown.

Kinetics↗
PubMed2006

Molecular statistics of cytochrome c: structural plasticity and molecular environment.

Nuclear magnetic resonance experiments performed on yeast mitochondrial cytochrome c (Cytc), a paradigmatic electron transfer protein, reveal that the two oxidation states have similar structures, but different mobility: despite the few structural differences compared with the reduced form, the oxidized form displays a larger unfolding propensity. Molecular dynamics simulations performed on both NMR reduced and NMR oxidized forms show that the reduced form has a larger solvent-accessible surface area (SASA). Starting from this observation, a molecular statistical approach was then applied in order to correlate the molecular surface to molecular mobility. Simulations started from biased initial conditions corresponding to different molecular sizes were combined with the maximal constrained entropy method. The NMR structure of oxidized Cytc is more suited to expose a smaller SASA than the NMR structure of the reduced form, but the accessible conformational landscape at 300 K around the NMR oxidized structure is flatter than for the NMR reduced structure. Protein configurations of smaller SASA and size display larger plasticity when they resemble the NMR oxidized structure, whereas they are more rigid when they resemble the NMR reduced structure. Implications of the results for the protein properties during its functional process are discussed.

Computer Simulation↗
PubMed2006

Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor.

It is well known that G protein-coupled receptors are prime targets for drug discovery. At the present time there is only one protein from this class that has an X-ray crystal structure, bovine rhodopsin. Crystal structures of rhodopsin have become invaluable templates for the modeling of class-A G protein-coupled receptors as they likely represent the overall topology of this family of proteins. However, because of low sequence homology within the class and the inherent mobility of integral membrane proteins, it is unlikely that this single structural template reflects the ensemble of conformations accessible for any given receptor. We have devised a procedure based upon comparative modeling that uses induced fit modeling coupled with binding site expansion. The modeling protocol enables an ensemble approach to binding mode prediction. The utility of models for beta-2 adrenergic receptor will be discussed.

Amino Acid Motifs↗
PubMed1989

Immunological analysis of porin polymorphism in Escherichia coli B and K-12.

Two sets of monoclonal antibodies (MoF type I and MoF type II) directed against the OmpF protein were used to analyze the immunological reactivity of the major outer membrane porins of E. coli B and K-12. All these antibodies present a specificity to the native OmpF protein. In addition, among the type II antibodies, MoF 18, 19 and 20 could recognize an epitope present on both monomeric and trimeric forms of the porin as demonstrated by immunoblotting analyses. The use of two different screening methods led to the isolation of two different sets of MoF, one specific for a native conformation accessible only on E. coli B strain and the second directed against epitopes present on OmpF of the two strains, B and K-12. These various responses are discussed in relation to the lipopolysaccharide binding to OmpF and with respect to the screening test used.

Antibodies, Monoclonal↗
PubMed2005

Aza-retinoids as novel retinoid X receptor-specific agonists.

A new structurally simple series of potent lipophilic aza-retinoids RXR agonists has been developed. SAR studies for the N-alkyl-azadienoic acids described here demonstrate that the RXR activity profile is sensitive to the N-alkyl chain length. Further, we have expanded the work to include azadienoic acids, which exhibited many accessible conformations leading to a better understanding of the SAR around the series.

Aza Compounds↗
PubMed2006

Recombinant Thermus aquaticus RNA polymerase for structural studies.

Advances in the structural biology of bacterial transcription have come from studies of RNA polymerases (RNAPs) from the thermophilic eubacteria Thermus aquaticus (Taq) and Thermus thermophilus (Tth). These structural studies have been limited by the fact that only endogenous Taq or Tth RNAP, laboriously purified from large quantities of Taq or Tth cell paste and offering few options for genetic modification, is suitable for structural studies. Recombinant systems for the preparation of Taq RNAP by co-overexpression and assembly in the heterologous host, Escherichia coli, have been described, but these did not yield enzyme suitable for crystallographic studies. Here we describe recombinant systems for the preparation of Taq RNAP harboring full or partial deletions of the Taq beta' non-conserved domain (NCD), yielding enzyme suitable for crystallographic studies. This opens the way for structural studies of genetically manipulated enzymes, allowing the preparation of more crystallizable enzymes and facilitating detailed structure/function analysis. Characterization of the Taqbeta'NCD deletion mutants generated in this study showed that the beta'NCD is important for the efficient binding of the sigma subunit, confirming previous hypotheses. Finally, preliminary structural analysis (at 4.1Angstroms resolution) of one of the recombinant mutants revealed a previously unobserved conformation of the beta-flap, further defining the range of conformations accessible to this flexible structural element.

Bacterial Proteins↗
PubMed2001

Single amino acid changes outside the active site significantly affect activity of glutathione S-transferases.

Glutathione S-transferases (GSTs: E.C. 2.5.1.18) are a multigene family of multifunctional dimeric proteins that play a central role in detoxication. Four allelic forms of the mosquito Anopheles dirus GST, adGST1-1, were cloned, expressed and characterized. The one or two amino acid changes in each allelic form was shown to confer different kinetic properties. Based on an available crystal structure, several of the residue changes were not in the putative substrate-binding pocket. Modeling showed that these insect Delta class GSTs also possess a hydrophobic surface pocket reported for Alpha, Mu and Pi class GSTs. The atom movement after replacement and minimization showed an average atom movement of about 0.1 A for the 0 to 25 A distance from the alpha carbon of the single replaced residue. This does not appear to be a significant movement in a static modeled protein structure. However, 200-500 atoms were involved with movements greater than 0.2 A. Dynamics simulations were performed to study the effects this phenomenon would exert on the accessible conformations. The data show that residues affecting nearby responsive regions of tertiary structure can modulate enzyme specificities, possibly through regulating attainable configurations of the protein.

Amino Acid Sequence↗
PubMed2004

Femtomole mixer for microsecond kinetic studies of protein folding.

We have developed a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 mus and sample consumption of femtomoles. This device enables us to access conformational changes under conditions far from equilibrium and at previously inaccessible time scales. In this paper, we discuss the design and optimization of the mixer using modeling of convective diffusion phenomena and a characterization of the mixer performance using microparticle image velocimetry, dye quenching, and Forster resonance energy-transfer (FRET) measurements of single-stranded DNA. We also demonstrate the feasibility of measuring fast protein folding kinetics using FRET with acyl-CoA binding protein.

Acyl Coenzyme A↗
PubMed1985

Theory for the folding and stability of globular proteins.

Using lattice statistical mechanics, we develop theory to account for the folding of a heteropolymer molecule such as a protein to the globular and soluble state. Folding is assumed to be driven by the association of solvophobic monomers to avoid solvent and opposed by the chain configurational entropy. Theory predicts a phase transition as a function of temperature or solvent character. Molecules that are too short or too long or that have too few solvophobic residues are predicted not to fold. Globular molecules should have a largely solvophobic core, but there is an entropic tendency for some residues to be "out of place", particularly in small molecules. For long chains, molecules comprised of globular domains are predicted to be thermodynamically more stable than spherical molecules. The number of accessible conformations in the globular state is calculated to be an exceedingly small fraction of the number available to the random coil. Previous estimates of this number, which have motivated kinetic theories of folding, err by many tens of orders of magnitude.

Mathematics↗
PubMed2006

Global effects of the energetics of coenzyme binding: NADPH controls the protein interaction properties of human cytochrome P450 reductase.

The thermodynamics of coenzyme binding to human cytochrome P450 reductase (CPR) and its isolated FAD-binding domain have been studied by isothermal titration calorimetry. Binding of 2',5'-ADP, NADP(+), and H(4)NADP, an isosteric NADPH analogue, is described in terms of the dissociation binding constant (K(d)), the enthalpy (DeltaH(B)) and entropy (TDeltaS(B)) of binding, and the heat capacity change (DeltaC(p)). This systematic approach allowed the effect of coenzyme redox state on binding to CPR to be determined. The recognition and stability of the coenzyme-CPR complex are largely determined by interaction with the adenosine moiety (K(d2)(')(,5)(')(-ADP) = 76 nM), regardless of the redox state of the nicotinamide moiety. Similar heat capacity change (DeltaC(p)) values for 2',5'-ADP (-210 cal mol(-)(1) K(-)(1)), NADP(+) (-230 cal mol(-)(1) K(-)(1)), and H(4)NADP (-220 cal mol(-)(1) K(-)(1)) indicate no significant contribution from the nicotinamide moiety to the binding interaction surface. The coenzyme binding stoichiometry to CPR is 1:1. This result validates a recently proposed one-site kinetic model [Daff, S. (2004) Biochemistry 43, 3929-3932] as opposed to a two-site model previously suggested by us [Gutierrez, A., Lian, L.-Y., Wolf, C. R., Scrutton, N. S., and Roberts, C. G. K. (2001) Biochemistry 40, 1964-1975]. Calorimetric studies in which binding of 2',5'-ADP to CPR (TDeltaS(B) = -13400 +/- 200 cal mol(-)(1), 35 degrees C) was compared with binding of the same ligand to the isolated FAD-binding domain (TDeltaS(B) = -11200 +/- 300 cal mol(-)(1), 35 degrees C) indicate that the number of accessible conformational substates of the protein increases upon 2',5'-ADP binding in the presence of the FMN-binding domain. This pattern was consistently observed along the temperature range that was studied (5-35 degrees C). This contribution of coenzyme binding energy to domain dynamics in CPR agrees with conclusions from previous temperature-jump studies [Gutierrez, A., Paine, M., Wolf, C. R., Scrutton, N. S., and Roberts, G. C. K. (2002) Biochemistry 41, 4626-4637]. A combination of calorimetry and stopped-flow spectrophotometry kinetics experiments showed that this linkage between coenzyme binding energetics and diffusional domain motion impinges directly on the molecular recognition of cytochrome c by CPR. Single-turnover reduction of cytochrome c by CPR (k(max) = 15 s(-)(1), K(d) = 37 microM) is critically coupled to coenzyme binding through ligand-induced motions that enable the FMN-binding domain to overcome a kinetically unproductive conformation. This is remarkable since the FMN-binding domain is not directly involved in coenzyme binding, the NADP(H) binding site being fully contained in the FAD-binding domain. Sequential rapid mixing measurements indicate that harnessing of coenzyme binding energy to the formation of a kinetically productive CPR-cytochrome c complex is a highly synchronized event. The inferred half-time for the decay of this productive conformation (tau(50)) is 330 +/- 70 ms only. Previously proposed structural and kinetic models are discussed in light of these findings.

Adenosine Diphosphate↗
PubMed2006

Structural energetics and base-pair opening dynamics in sarcin-ricin domain RNA.

The sarcin-ricin domain is a universal element of the RNA from the large ribosomal subunit. The domain is part of the binding site for elongation factors and is specifically cleaved by the toxins alpha-sarcin and ricin. In this work, we have mapped the energetics and dynamics of individual structural motifs in a 29-mer RNA oligomer containing the sarcin-ricin domain. The stability of individual base pairs in the structure was characterized from measurements of the exchange rates of imino protons using nuclear magnetic resonance spectroscopy at 10 degrees C. The measurements also provided the rates of opening and closing for selected base pairs. The results reveal that the structural stabilization free energies in the sarcin-ricin domain are broadly distributed between 2.9 and 10.6 kcal/mol. One of the least stable sites in the structure is the noncanonical G-A base pair located next to the phosphodiester bond that is cleaved by alpha-sarcin. The low stability of this base pair supports the proposal that cleavage by alpha-sarcin occurs by a base flipping mechanism. The opening dynamics of other base pairs is affected by elements of the structure such as the bulged-G motif and its cross-strand stacking. Participation in these motifs increases the lifetimes of the bases in an open, solvent-accessible conformation.

Animals↗
PubMed1998

An EPR Study of 2,3-Bis(diphenylphosphino)maleic Anhydride (BMA) Complexes and the BMA Radical Anion.

EPR spectra are reported for four metal complexes of 2,3-bis(diphenylphosphino)maleic anhydride (BMA), [Co(2)(PhCCR)(CO)(4)(eta-BMA)](-), R = Ph, H, [Co(2)(PhCCPh)(CO)(4)(&mgr;-BMA)](-), and [PhCW(CO)(2)(BMA)Cl](-), as well as the radical anions, [BMA](-) and [BPCD](-), BPCD = 4,5-bis(diphenylphosphino)cyclopentene-1,3-dione. At room temperature, all spectra are 1:2:1 triplets due to hyperfine coupling to two equivalent (31)P nuclei with coupling to two equivalent (1)H nuclei for [BPCD](-) and unresolved coupling to one or two (59)Co nuclei for the Co complexes with chelating or bridging BMA, respectively. The (31)P couplings are temperature dependent, ca. -3 and -13 mG K(-)(1) for the metal complexes and ligand radical anions, respectively. At low temperature, the spectrum of [BMA](-) shows the presence of symmetric and asymmetric PPh(2) rotational conformers, related by the thermodynamic parameters DeltaH degrees = -0.8 +/- 0.2 kJ mol(-)(1) and DeltaS degrees = 4 +/- 1 J mol(-)(1) K(-)(1) and interconverted with activation parameters DeltaH() = 18.2 +/- 0.4 kJ mol(-)(1), DeltaS() = -30 +/- 2 J mol(-)(1) K(-)(1). The temperature dependence of the (31)P couplings is explained by a negative spin-polarization contribution to and a positive contribution due to P 3s character; the latter increases with the asymmetry of the PPh(2) conformations. The range of conformations accessible to the metal complexes is less than for the ligand radical anions, and accordingly the temperature dependence is significantly smaller.

Journal Article↗
PubMed2005

On the origin of the thermostabilization of proteins induced by sodium phosphate.

The B1 domain of protein L shows a linear rise in thermostability with increasing concentrations of sodium phosphate. Equal behavior is observed for a set of mutant proteins where surface lysines are mutated to noncharged residues, but the mutant's thermostabilities show different sensitivities to phosphate, encoded in the varying slopes observed (mi). The melting temperature in the absence of the cosolute also correlates linearly with mi. The stabilizing effect of the phosphate ion reaches a saturation point, which has been experimentally determined for protein L (1610 mM phosphate). These results indicate that the phosphate-induced stabilization is an inherent property of the protein, encoded in the amino acid sequence. Changes in stability upon mutation are attributed to a redistribution of the overall network of solvated surface charges. Stabilization by phosphate is understood in terms of interactions with the protein surface, reducing the unfavorable contacts between like charges, maximizing the number of accessible conformations of the surface-charged side chains, and optimizing solvation.

Bacterial Proteins↗
PubMed1992

Modeling of competitive phosphono amino acid NMDA receptor antagonists.

A pharmacophore for the phosphono amino acid antagonists of the NMDA receptor has been developed using computer-based molecular modeling techniques. An important feature of this model is that a single binding site is proposed for the phosphonic acid moiety. All competitive antagonists we have examined incorporating amino acid and phosphonate groups in their structure fit the pharmacophore in energetically accessible conformations.

Binding, Competitive↗
PubMed2004

Thermostability of protein studied by molecular dynamics simulation.

The thermostability of protein thermostable cathechol 2,3-dixoygenase (TC23O) has been studied by the parallel molecular dynamics simulations. By analysis of the exponent beta, which is related to the scattering spectrum and constant-pressure heat capacity Cp, we reveal the respective contribution of a specific residue 228 proline; a specific salt bridge, Lys188N-Glu291OE1; four ions; and a different water environment to the thermostability of TC23O. The dynamic transition temperature of the mutants, Pro228Ser and Glu291Gly of the TC23O, was decreased about 10 degrees C and 19 degrees C respectively. The displacement of the four ions had no significant effect on the thermostability of TC23O. Water affects the thermostability by influencing the changes of accessible conformation to a certain extent. All these results agree with the known experimental results.

Catechol 2,3-Dioxygenase↗