Multiple active site conformers in the carbon monoxide complexes of trematode hemoglobins

Sequence alignment of hemoglobins of the trematodes Paramphistomum epiclitum and Gastrothylax crumenifer with myoglobin suggests the presence of an unusual active site structure in which two tyrosine residues occupy the E7 and B10 helical positions. In the crystal structure of P. epiclitum hemoglobin, such an E7-B10 tyrosine pair at the putative helical positions has been observed, although the E7 Tyr is displaced toward CD region of the polypeptide. Resonance Raman data on both P. epiclitum and G. crumenifer hemoglobins show that interactions of heme-bound ligands with neighboring amino acid residues are unusual. Multiple conformers in the CO complex, termed the C, O, and N conformers, are observed. The conformers are separated by a large difference (approximately 60 cm(-1)) in the frequencies of their Fe-CO stretching modes. In the C conformer the Fe-CO stretching frequency is very high, 539 and 535 cm(-1), for the P. epiclitum and G. crumenifer hemoglobins, respectively. The Fe-CO stretching of the N conformer appears at an unusually low frequency, 479 and 476 cm(-1), respectively, for the two globins. A population of an O conformer is seen in both hemoglobins, at 496 and 492 cm(-1), respectively. The C conformer is stabilized by a strong polar interaction of the CO with the distal B10 tyrosine residue. The O conformer is similar to the ones typically seen in mutant myoglobins in which there are no strong interactions between the CO and residues in the distal pocket. The N conformer possesses an unusual configuration in which a negatively charged group, assigned as the oxygen atom of the B10 Tyr side chain, interacts with the CO. In this conformer, the B10 Tyr assumes an alternative conformation consistent with one of the conformers seen the crystal structure. Implications of the multiple configurations on the ligand kinetics are discussed.     

Queuosine metabolism: possible relation to B-cell activation by C8 derivatives of guanosine

The observed enhancement of B-lymphocyte activation by 8-bromoguanosine and 8-mercaptoguanosine is hypothesized to occur via a "binding protein" which requires a guanine nucleoside as the syn conformer for productive interaction. In addition, because of the 7-substituent, Q nucleoside also is hypothesized to bind as the syn conformer and, therefore, to be a potential B-lymphocyte activator.     

A folded (10 S) conformer of myosin from a striated muscle and its implications for regulation of ATPase activity.

Myosin from the striated adductor muscle of the scallop Pecten maximus is shown to fold into a compact 10 S conformer under relaxing conditions, as has been characterized for smooth and non-muscle myosins. The folding transition is accompanied by the trapping of nucleotide at the active site to give a species with a half-life of about an hour at 20 degrees C. Ca2+ binding to the specific, regulatory sites on a myosin head promotes unfolding to the extended 6 S conformer and activates product release by 60-fold. The unfolding transition, however, remains much slower than the contraction-relaxation cycle of scallop striated muscle and could not play a role in the regulation of these events. The dissociation of products from myosin heads in native thick filaments is Ca2(+)-regulated, but under relaxing conditions the nucleotide is released at least an order of magnitude faster than from the 10 S monomeric myosin, at a rate similar to that observed with heavy meromyosin. Thus, there is no evidence for any intermolecular interaction between neighbouring molecules in the filament analogous to the head-neck intramolecular interaction in the 10 S conformer. It is possible that the 10 S myosin state represents an inert form involved in the control of filament assembly during muscle growth and development. Removal of regulatory light chains or labelling the reactive heavy chain thiol of myosin prevents, or at least disfavours, formation of the folded 10 S conformer and allows separation of the modified protein from the native molecules.     

Calculation of the conformation of glycosphingolipids. 2. GM1- and GM2-gangliosides

The conformations of GM1- and GM2-gangliosides have been predicted by energy minimization techniques including an orbital force field approach. The global energy minimum conformers for these two gangliosides show marked differences, particularly in the relative orientation of the sugar rings. The predicted structures are compared with those postulated from NMR spectroscopy in relation to the formation of a cation-binding site. The minimum energy conformer of GM2-ganglioside is able to form this binding site whereas this conformer of GM1-ganglioside is not. The nature of the specific interaction of gangliosides with activator proteins is discussed.     

Stabilization of (dG-dC)n.(dG-dC)n in the Z conformation by a crosslinking reaction

(dG-dC)n.(dG-dC) was converted to the Z conformer by heating in the presence of Mn++n. Reaction of this preparation with the crosslinking reagent, DL-diepoxybutane (DEB), stabilized this conformer so that it retained its structure even when returned to conditions that favored reversion to the B conformation. Treatment of the crosslinked Z conformer with periodate caused scission of the crosslink, allowing reversion to the B conformer. Reaction of (dG-dC)n.(dG-dC)n in the B conformation with DEB did not prevent conversion to the Z conformer in 4M NaC1; dialysis of the high salt solution against low ionic strength buffer allowed return to the B conformer. The Z in equilibrium B transitions were followed by circular dichroism studies and immunochemical procedures. The results suggest the feasibility of stabilizing Z sequences of DNA in chromatin by crosslinking, so that they could then be identified after DNA isolation.     

Intramolecular and intermolecular interactions of protein kinase B define its activation in vivo

Protein kinase B (PKB/Akt) is a pivotal regulator of diverse metabolic, phenotypic, and antiapoptotic cellular controls and has been shown to be a key player in cancer progression. Here, using fluorescent reporters, we shown in cells that, contrary to in vitro analyses, 3-phosphoinositide–dependent protein kinase 1 (PDK1) is complexed to its substrate, PKB. The use of Förster resonance energy transfer detected by both frequency domain and two-photon time domain fluorescence lifetime imaging microscopy has lead to novel in vivo findings. The preactivation complex of PKB and PDK1 is maintained in an inactive state through a PKB intramolecular interaction between its pleckstrin homology (PH) and kinase domains, in a “PH-in” conformer. This domain–domain interaction prevents the PKB activation loop from being phosphorylated by PDK1. The interactive regions for this intramolecular PKB interaction were predicted through molecular modeling and tested through mutagenesis, supporting the derived model. Physiologically, agonist-induced phosphorylation of PKB by PDK1 occurs coincident to plasma membrane recruitment, and we further shown here that this process is associated with a conformational change in PKB at the membrane, producing a “PH-out” conformer and enabling PDK1 access the activation loop. The active, phosphorylated, “PH-out” conformer can dissociate from the membrane and retain this conformation to phosphorylate substrates distal to the membrane. These in vivo studies provide a new model for the mechanism of activation of PKB. This study takes a crucial widely studied regulator (physiology and pathology) and addresses the fundamental question of the dynamic in vivo behaviour of PKB with a detailed molecular mechanism. This has important implications not only in extending our understanding of this oncogenic protein kinase but also in opening up distinct opportunities for therapeutic intervention.     

Sequence-dependent folding of DNA three-way junctions

Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined by the DNA sequence. In this study we have compared several three-way DNA junctions in order to assess how the arrangement of bases around the branch point affects the conformer distribution. The results show that rearranging the different arms, while retaining their base sequences, can affect the conformer distribution. In some instances this generates a structure that appears to contain parallel coaxially stacked helices rather than the usual anti-parallel arrangement. Although the conformer equilibrium can be affected by the order of purines and pyrimidines around the branch point, this is not sufficient to predict the conformer distribution. We find that the folding of three-way junctions can be separated into two groups of dinucleotide steps. These two groups show distinctive stacking properties in B-DNA, suggesting there is a correlation between B-DNA stacking and coaxial stacking in DNA junctions.     

Structural recognition of an ICAM-1 peptide by its receptor on the surface of T cells: conformational studies of cyclo (1, 12)-Pen-Pro-Arg-Gly-Gly-Ser-Val-Leu-Val-Thr-Gly-Cys-OH.

The purpose of this study is to elucidate the solution conformation of cyclic peptide 1 (cIBR), cyclo (1, 12)-Pen1-Pro2-Arg3-Gly4-Gly5-Ser6-Val7-Leu8-V al9-Thr10-Gly11-Cys12-OH, using NMR, circular dichroism (CD) and molecular dynamics (MD) simulation experiments. cIBR peptide (1), which is derived from the sequence of intercellular adhesion molecule-1 (ICAM-1, CD54), inhibits homotypic T-cell adhesion in vitro. The peptide hinders T-cell adhesion by inhibiting the leukocyte function-associated antigen-1 (LFA-1, CD11a/CD18) interaction with ICAM-1. Furthermore, Molt-3 T cells bind and internalize this peptide via cell surface receptors such as LFA-1. Peptide internalization by the LFA-1 receptor is one possible mechanism of inhibition of T-cell adhesion. The recognition of the peptide by LFA-1 is due to its sequence and conformation; therefore, this study can provide a better understanding for the conformational requirement of peptide-receptor interactions. The solution structure of 1 was determined using NMR, CD and MD simulation in aqueous solution. NMR showed a major and a minor conformer due to the presence of cis/trans isomerization at the X-Pro peptide bond. Because the contribution of the minor conformer is very small, this work is focused only on the major conformer. In solution, the major conformer shows a trans-configuration at the Pen1-Pro2 peptide bond as determined by HMQC NMR. The major conformer shows possible beta-turns at Pro2-Arg3-Gly4-Gly5, Gly5-Ser6-Val7-Leu8, and Val9-Thr10-Gly11-Cys12. The first beta-turn is supported by the ROE connectivities between the NH of Gly4 and the NH of Gly5. The connectivities between the NH of Ser6 and the NH of Val7, followed by the interaction between the amide protons of Val7 and Leu8, support the presence of the second beta-turn. Furthermore, the presence of a beta-turn at Val9-Thr10-Gly11-Cys12 is supported by the NH-NH connectivities between Thr10 and Gly11 and between Gly11 and Cys12. The propensity to form a type I beta-turn structure is also supported by CD spectral analysis. The cIBR peptide (1) shows structural similarity at residues Pro2 to Val7 with the same sequence in the X-ray structure of D1-domain of ICAM-1. The conformation of Pro2 to Val7 in this peptide may be important for its binding selectivity to the LFA-1 receptor.     

Regulatory mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae. II. Theory

In this study, rate equations that predict the regulatory kinetic behavior of homocitrate synthase were derived, and simulation of the predicted behavior was carried out over a range of values for the kinetic parameters. The data obtained allow application of the resulting expressions to enzyme systems that exhibit activation and inhibition as a result of the interaction of effectors at multiple sites in the free enzyme. Homocitrate synthase was used as an example in terms of its activation by Na+ binding to the active enzyme conformer at an allosteric site, inhibition by binding to the active site, and inhibition by lysine binding to the less active enzyme conformer.     

The interconversion of conformers of phenylalanyl-tRNA with different affinity to 70S ribosomes of Escherichia coli.

Earlier the existence of two conformers of Phe-tRNAPhe of E. coli was demonstrated because one of them yields complexes with 70S-poly(U) of extremely high affinity and the other with at least a 105 lower binding constant. We denote the first conformer as HAC (high affinity conformer) and the second as LAC (low affinity conformer). This high difference in binding constants was used for studying the process of reversible interconversion of conformers of Phe-tRNAPhe. The transition kinetics of LAC to HAC in conditions when the latter is stable (in the presence of magnesium ions) was studied and a high value of activation energy (35 kcal/mole) found. The interconversion is the first order reaction and equilibrium does not depend of overall Phe-tRNA concentration.     

Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif

Identification of sequence motifs that favor cis peptide bonds in proteins is important for understanding and designing proteins containing turns mediated by cis peptide conformations. From (1)H NMR solution studies on short peptides, we show that the Pro-Pro peptide bond in Pro-Pro-Phe almost equally populates the cis and trans isomers, with the cis isomer stabilized by a CHc...pi interaction involving the terminal Pro and Phe. We also show that Phe is over-represented at sequence positions immediately following cis Pro-Pro motifs in known protein structures. Our results demonstrate that the Pro-Pro cis conformer in Pro-Pro-Phe sequence motifs is as important as the trans conformer, both in short peptides as well as in natively folded proteins.     

A study of conformational states of substrates of cytochrome P450 3A4

A multiconformational study of substrates of cytochrome P450 3A4 has been carried out within the BiS/MC algorithm. The method allowed one to create a pseudoatomic model of the cytochrome and to find the substrate conformers responsible for the interaction with the cytochrome. It has been found that, in most cases, the geometry of the acting conformer is much different from the geometry of the global minimum conformer. It has been shown that the mirror conformational antipodes ("enantioconformers") are characterized as a rule by different Michaelis constants. A quantitative relationship between the Michaelis constants and the parameters of interactions in "model 3A4 isoform-substrate" complexes has been determined. The relationship describes the experimental value of Michaelis constant with the squared cross-validation correlation coefficient of 0.88.     

A study of conformational states of substrates of isoform 3A4 of cytochrome P450

A multiconformational study of substrates for isoform 3A4 of cytochrome P450 with the use of the BiS/MC algorithm has been carried out. The use of this approach made it possible to determine the pseudo-atomic model of this cytochrome and to find the substrate conformers responsible for binding to the cytochrome. It was found that in most cases, the geometry of the conformer, which is bound to the isoform, substantially differs from the geometry of the global minimum conformer. It was shown that, as a rule, the mirror antipodes (enantioconformers) are characterized by different Michaelis constants. The quantitative relationship of the Michaelis constants with the parameters of interaction in the model complexes between the isoform 3A4 and substrates was determined. This dependence describes an experimental value of the Michaelis constant with a squared cross-validation correlation coefficient of 0.88, which was determined by leave-one-out cross-validation technique.     

Conformational analysis of an opioid peptide in solvent media that mimic cytoplasm viscosity.

Many neuropeptides exert their action between the presynaptic vesicles and postsynaptic transmembrane receptors, crossing different layers of specialized cytoplasm. Biomimetic media usually employed to study bioactive peptides do not reproduce the physico chemical environment of cytoplasm--in particular, the high viscosity of this biological fluid. Here we describe a conformational study of a delta-selective opioid peptide, deltorphin I, at variable temperatures in several biocompatible media characterized by varying values of viscosity and dielectric constant. It was found that only viscosity, among these parameters, induces ordered conformations; that is, it acts as a conformational sieve. This finding suggests that the high viscosity of the intersynaptic fluid contributes, in addition to the membrane catalysis proposed by Schwyzer, in overcoming the so-called entropic barrier to the transition state of peptide-receptor interaction by selecting ordered conformations prior to receptor interaction. The folded conformer found in the 80:20 (v:v) DMSOd6/H2O cryoprotective mixture at 265 K has a shape consistent with those of rigid nonpeptidic opiates.     

Mechanism divergence in microbial rhodopsins

A fundamental design principle of microbial rhodopsins is that they share the same basic light-induced conversion between two conformers. Alternate access of the Schiff base to the outside and to the cytoplasm in the outwardly open “E” conformer and cytoplasmically open “C” conformer, respectively, combined with appropriate timing of pKa changes controlling Schiff base proton release and uptake make the proton path through the pumps vectorial. Phototaxis receptors in prokaryotes, sensory rhodopsins I and II, have evolved new chemical processes not found in their proton pump ancestors, to alter the consequences of the conformational change or modify the change itself. Like proton pumps, sensory rhodopsin II undergoes a photoinduced E → C transition, with the C conformer a transient intermediate in the photocycle. In contrast, one light-sensor (sensory rhodopsin I bound to its transducer HtrI) exists in the dark as the C conformer and undergoes a light-induced C → E transition, with the E conformer a transient photocycle intermediate. Current results indicate that algal phototaxis receptors channelrhodopsins undergo redirected Schiff base proton transfers and a modified E → C transition which, contrary to the proton pumps and other sensory rhodopsins, is not accompanied by the closure of the external half-channel. The article will review our current understanding of how the shared basic structure and chemistry of microbial rhodopsins have been modified during evolution to create diverse molecular functions: light-driven ion transport and photosensory signaling by protein–protein interaction and light-gated ion channel activity.     

Isoelectric focusing of interacting systems. II. pH-dependent conformational transitions.

Transient and equilibrium isoelectric focusing patterns have been computed for pH-dependent conformational transitions in the limits of complete cooperativity and instantaneous chemical equilibration. Transitions induced by the binding of a relatively large number of hydrogen ions by the macromolecule give well resolved bimodal equilibrium patterns, provided that the resulting conformer has the lower isoelectric point. The corresponding transient patterns may be either bimodal or virtually unimodal for practical times of operation depending upon the point of insertion of the sample into the pH gradient and the stoichiometry of the interaction. A macromolecule undergoing sequential transitions can give multimodal isoelectric focussing patterns.     

Thermodynamics and kinetics of formation of the alkaline state of a Lys 79-->Ala/Lys 73-->His variant of iso-1-cytochrome c

The alkaline transition kinetics of a Lys 73-->His (H73) variant of iso-1-cytochrome c are triggered by three ionizable groups [Martinez, R. E., and Bowler, B. E. (2004) J. Am. Chem. Soc. 126, 6751-6758]. To eliminate ambiguities caused by overlapping phases due to formation of the Lys 79 alkaline conformer and proline isomerization associated with the His 73 alkaline conformer, we mutated Lys 79 to Ala in the H73 variant (A79H73). The stability and guanidineHCl m-values of the A79H73 and H73 variants at pH 7.5 are the same. The Ala 79 mutation causes formation of the alkaline conformer to depend on [NaCl]. The salt dependence saturates at 500 mM NaCl, and the thermodynamics of alkaline state formation for the A79H73 and H73 variants become identical. The salt dependence is consistent with loss of an electrostatic contact between Lys 79 and heme propionate D in the A79H73 variant. The kinetics of alkaline state formation for the A79H73 variant support the three trigger group model developed for the H73 variant, with the primary trigger, pK(HL), being ionization of His 73. The low pH ionization, pK(H1), is perturbed by the Ala 79 mutation indicating that this ionization is modulated by the buried hydrogen bond network involving heme propionate D. The A79H73 variant has a high spin heme above pH 9 suggesting that the high pH ionization, pK(H2), involves a high spin heme conformer. The proline isomerization phase is modulated by both pK(HL) and pK(H2) indicating that it is sensitive to protein conformation.     

High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase

A high-pressure (15)N/(1)H two-dimensional NMR study has been carried out on folate-bound dihydrofolate reductase (DHFR) from Escherichia coli in the pressure range between 30 and 2000 bar. Several cross-peaks in the (15)N/(1)H HSQC spectrum are split into two with increasing pressure, showing the presence of a second conformer in equilibrium with the first. Thermodynamic analysis of the pressure and temperature dependencies indicates that the second conformer is characterized by a smaller partial molar volume (DeltaV = -25 mL/mol at 15 degrees C) and smaller enthalpy and entropy values, suggesting that the second conformer is more open and hydrated than the first. The splittings of the cross-peaks (by approximately 1 ppm on (15)N axis at 2000 bar) arise from the hinges of the M20 loop, the C-helix, and the F-helix, all of which constitute the major binding site for the cofactor NADPH, suggesting that major differences in conformation occur in the orientations of the NADPH binding units. The Gibbs free energy of the second, open conformer is 5.2 kJ/mol above that of the first at 1 bar, giving an equilibrium population of about 10%. The second, open conformer is considered to be crucial for NADPH binding, and the NMR line width indicates that the upper limit for the rate of opening is 20 s(-)(1) at 2000 bar. These experiments show that high pressure NMR is a generally useful tool for detecting and analyzing "open" structures of a protein that may be directly involved in function.     

Downhill versus Barrier-Limited Folding of BBL: 3. Heterogeneity of the Native State of the BBL Peripheral Subunit Binding Domain and Its Implications for Folding Mechanisms

Protein folding studies are generally predicated on Anfinsen's dogma that there is a unique native state of a protein. However, this is not always the case. NMR measurements of BBL, for example, find a decrease in helicity of helix 2 surrounding His166 on its protonation, which, with other experimental data, suggests that the native state can occupy two or more conformations. Here, we analysed the native structure of BBL as a function of pH, temperature and ionic strength, along with a truncated BBL construct, by extensive all-atom molecular dynamics simulations in explicit solvent, corresponding to at least 400 ns of trajectories collected for each set of conditions. The native state was heterogeneous under a variety of conditions, consisting of two predominant conformations. This equilibrium changed with conditions: protonation of His166 at low pH shifted the equilibrium in favour of a less ordered conformer, while high ionic strength at neutral pH shifted the equilibrium to a more ordered conformer. Furthermore, high temperature and truncation of the sequence also shifted the equilibrium toward the less ordered conformer. Importantly, conformational heterogeneity in a native structure that changes with conditions will lead to deviations from the classic two-state behaviour during the barrier-limited unfolding of a protein. In particular, some regions of the protein will appear to unfold asynchronously and some residues will have anomalous thermal titration curves and unusual baseline behaviour monitored microscopically by NMR spectroscopy and macroscopically by calorimetry and other techniques. Such data could otherwise be interpreted as evidence for barrier-free downhill folding. Any biological significance of downhill folding of BBL appears to be ruled out by recent crystallographic studies on the reaction cycle of the BBL-equivalent domain in a pyruvate dehydrogenase multienzyme complex in which the domain remains of constant structure.