Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Conformational accessibility”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,135 records · Page 63Linked to original sources

Probing the heme iron coordination structure of alkaline chloroperoxidase.

The mechanism by which the heme-containing peroxidase, chloroperoxidase, is able to chlorinate substrates is poorly understood. One approach to advance our understanding of the mechanism of the enzyme is to determine those factors which contribute to its stability. In particular, under alkaline conditions, chloroperoxidase undergoes a transition to a new, spectrally distinct form, with accompanying loss of enzymatic activity. In the present investigation, ferric and ferrous alkaline chloroperoxidase (C420) have been characterized by electronic absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopy. The heme iron oxidation state influences the transition to C420; the pKa for the alkaline transition is 7.5 for the ferric protein and 9.5 for the ferrous protein. The five-coordinate, high-spin ferric native protein converts to a six-coordinate low-spin species (C420) as the pH is raised above 7.5. The inability of ferric C420 to bind exogenous ligands, as well as the dramatically increased reactivity of the proximal Cys29 heme ligand toward modification by the sulfhydryl reagent p-mercuribenzoate, suggests that a conformational change has occurred during conversion to C420 that restricts access to the peroxide binding site while increasing the accessibility of Cys29. However, it does appear that Cys29-derived ligation is at least partially retained by ferric C420, potentially in a thiolate/imidazole coordination sphere. Ferrous C420, on the other hand, appears not to possess a thiolate ligand but instead likely has a bis-imidazole (histidine) coordination structure. The axial ligand trans to carbon monoxide in ferrous-CO C420 may be a histidine imidazole. Since chloroperoxidase functions normally through the ferric and higher oxidation states, the fact that the proximal thiolate ligand is largely retained in ferric C420 clearly indicates that additional factors such as the absence of a vacant sixth coordination site sufficiently accessible for peroxide binding may be the cause of catalytic inactivity.

Chloride Peroxidase↗

[Use of multimodality imagery in radiotherapy].

The quality of treatment that one can realize today in conformal radiotherapy, can be reached only if one has access to 3D imaging allowing a precise determination of the volume of the organs at risk and of the GTV. For this reason, one has access to anatomical imaging, CT or MRI, and functional and metabolic imaging, PET or SPECT imaging. CT gives the electronic density of the tissues, which is essential to ensure a very precise calculation of dose distribution. Its insufficiency in the visualization of the tumor and some anatomical structures makes necessary the registration of these images with MRI of which distortions are sufficiently weak to be usable in radiotherapy. The registration will be usable only if images of each modality are realized with the patient in treatment position, except for brain, where only CT, on which is based the registration, must be done in treatment position. At least, if one wants to visualize the active parts of a tumor or to make the difference between fibrosis and tumor left or recurrence after radiotherapy or chemotherapy, it is necessary to use PET or SPECT. To define correctly the CTV using these images, one must realize the anatomical localization of the metabolic abnormalities, which they highlight with a registration based on CT or MRI. The difficulties to obtain the registration of these images led the manufacturer to propose mixed machines allowing to realize, at the same time, a CT imaging and a PET or a SPECT imaging with the patient in treatment position.

Diagnostic Imaging↗

The role of the methionine residues in the structure and function of parathyroid hormone.

Forms of the biologically active N-terminal fragment of bovine parathyroid hormone oxidized at methionine 8, methionine 18, and both positions were prepared, separated from one another, and characterized as described earlier for the native hormone (A. L. Frelinger and J. E. Zull, (1984) J. Biol. Chem. 259, 5507). The biological properties of the oxidized forms were compared to those of the native hormone, using the renal membrane adenylyl cyclase assay. Oxidation at position 18 produced full agonists of the hormone with slightly reduced potency. Oxidation at position 8 produced partial agonists of greatly reduced potency. Oxidation at both positions produced partial agonists of even lower potency. Thus, methionine 8 is implicated both in binding and in activation of adenylyl cyclase, but methionine 18 is implicated only in binding. Further study showed that oxidation of both residues is dependent on the pH, ionic strength, and polarity of the solvent. However, methionine 8 is less easily oxidized than methionine 18. This difference is eliminated in 3 M guanidine-HCl with 1-34 and in 6 M guanidine-HCl with 1-84. On the other hand the difference in reactivity is greatly increased in high ionic strength, with methionine 8 becoming much less reactive. These results suggest that the methionine residues are important in the biologically active conformation of parathyroid hormone and that methionine 8 is less accessible than methionine 18 under certain conditions. These conclusions are discussed in the context of a specific model for the folding of parathyroid hormone.

Adenylyl Cyclases↗

A novel form of the plasminogen activator inhibitor created by cysteine mutations extends its half-life: relevance to cancer and angiogenesis.

Proteolytic activity driven by urokinase (uPA) is commonly recognized as an important factor in metastasis and angiogenesis. The eradication of unwanted uPA activity expressed by cancer cells results in the inhibition of metastasis and angiogenesis. Development of novel and highly selective uPA inhibitors could, therefore, produce new treatments of cancer. The ultimate goal of this work is the identification of novel and selective inhibitors of uPA suitable for this purpose. We have chosen plasminogen activator inhibitor(s) type 1 (PAI-1), which selectively inhibits the urokinase plasminogen activator (uPA). However, PAI-1 is not a stable molecule and converts itself into the latent form with a half-life in the range of t1/2 = 1-2 h. This conversion is associated with a partial insertion of the reactive loop (P4-P10') into the PAI-1 molecule. In such a conformation, P1-P1' and other sites are not accessible for reaction with uPA. To conquer this hurdle, we have produced several PAI-1 mutants by replacing chosen amino acids with cysteine in the hope of creating disulfide bridges, which could make this insertion more difficult. On the basis of the known structure of active PAI-1, we have identified amino acids that can be substituted with a cysteine residue to produce disulfide bridges linking the top and bottom parts of strands A3 and A5 as well as sites within the helix-D region. We created a total of seven cysteine mutants via point mutation (two to six point mutations), generating possible sites for disulfide bridge formation at the top and bottom parts of A3 and A5, within the helix-D region, or by a combination thereof. Desired mutations were introduced by PCR using appropriate primers. The mutant forms of PAI-1 containing the chitin-binding intein tag were then purified using affinity chromatography wherein the intein tag is cleaved, leaving mutant PAI-1 protein. Cys mutations resulted in proteins with extended half-life of PAI-1 from 2 to >700 h depending on the mutant. Novel PAI-1 were fully functional against uPA and showed activity in the in vitro model of angiogenesis, e.g., in the inhibition of sprout formation. Such prolonged serpin activity, which is therapeutically desired in cancer treatment and Cys-mutated PAI-1, could launch a new class of novel anticancer agents.

Amino Acid Sequence↗

Further requirements for cleavage by the murine coronavirus 3C-like proteinase: identification of a cleavage site within ORF1b.

The coronavirus mouse hepatitis virus strain A59 (MHV-A59) encodes a 3C-like proteinase (3CLpro) that is proposed to be responsible for the majority of the processing events that take place within the replicase polyproteins pp1a and pp1ab. In this study we demonstrate that the Q939/S940 peptide bond, located between the polymerase and Zn-finger regions of pp1ab (the POL/Zn site), is processed by the 3CLpro, albeit inefficiently. Mutagenesis of the POL/Zn site, as well as the previously identified HD1/3C site in the 1a region of pp1a and pp1ab, demonstrated that the amino acid residues at the P2 and P1 positions of the cleavage site, occupied by L and Q, respectively, were important determinants of 3CLpro substrate specificity. Finally, a direct comparison of the 3CLpro-mediated cleavages at the HD1/3C and POL/Zn sites was made by determining the rate constants using synthetic peptides. The results show that while a larger polypeptide substrate carrying the HD1/3C site was processed more efficiently than a polypeptide substrate carrying the POL/Zn site, cleavage of the synthetic peptide substrates containing these two cleavage sites occurred at similar efficiencies. This indicates that the overall conformation of a large polyprotein substrate is important in the accessibility of the cleavage site to the proteinase.

Amino Acid Sequence↗

Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations.

Molecular dynamics trajectories were calculated separately for each of the two molecules in the asymmetric unit of the crystal structure of the hemoprotein domain of cytochrome P450BM-3. Each simulation was 200 ps in length and included a 10 A layer of explicit solvent. The simulated time-average structure of each P450BM-3 molecule is closer to its crystal structure than the two molecular dynamics time-averaged structures are to each other. In the crystal structure, molecule 2 has a more accessible substrate binding pocket than molecule 1, and this difference is maintained throughout the simulations presented here. In particular, the substrate docking regions of molecule 1 and molecule 2 diverge in the solution state simulations. The mouth of the substrate binding pocket is significantly more mobile in the simulation of molecule 2 than in the simulation of molecule 1. For molecule 1, the width of the mouth is only slightly larger than its X-ray value of 8.7 A and undergoes fluctuations of about 1 A. However, in molecule 2, the mouth of the substrate binding pocket is dramatically more open in the time-average molecular dynamics structure (14.7 A) than in the X-ray structure (10.9 A). Furthermore, this region of the protein undergoes large amplitude motions during the trajectory that are not seen in the trajectory of molecule 1, repeatedly opening and closing up to 7 A. Presumably, the binding of different substrates will induce the mouth region to adopt different conformations from within the wide range of structures that are accessible.

Binding Sites↗

[Contribution of registered and/or fused images to radiotherapy].

The quality of treatment that one can realize today in conformal radiotherapy, can be reached only if one has access to 3D imaging allowing a precise determination of the volume of the organs at risk and of the GTV. For this reason, one has access to anatomical imaging, CT or MRI, and functional and metabolic imaging, PET or SPECT imaging. CT gives the electronic density of the tissues, which is essential to ensure a very precise calculation of dose distribution. Its insufficiency in the visualization of the tumour and some anatomical structures makes necessary the registration of these images with MRI of which distortions are sufficiently weak to be usable in radiotherapy. The registration will be usable only if images of each modality are realised with the patient in treatment position, except for brain, where only CT, on which is based the registration, must be done in treatment position. The images registration is also called images fusion by some authors. Others consider fusion of images as a way to display registered images on a screen, specially for CT images and PET, and MRI and SPECT. Nevertheless, the fusion of images is a function offered by some softwares. It allows obtaining a single volume of voxels from those of the registered images (CT and MR images). This volume is not usable in radiotherapy because it keeps only partially the contributions of the CT scan images and the MRI. At least, if one wants to visualize the active parts of a tumour or to make the difference between fibrosis and tumour left or recurrence after radiotherapy or chemotherapy, it is necessary to use PET or SPECT. To define correctly the CTV using these images, one must realize the anatomical localization of the metabolic abnormalities, which they highlight with a registration based on CT or MRI. The difficulties to obtain the registration of these images led the manufacturer to propose mixed machines allowing realizing, at the same time, a CT imaging and a PET or a SPECT imaging with the patient in treatment position.

Humans↗

Peptide design: influence of a guest Aib-Pro segment on the stereochemistry of an oligo-val sequence--solution conformations and crystal structure of Boc-(Val)2-Aib-Pro-(Val)3-OMe.

The peptide Boc-Val-Val-Aib-Pro-Val-Val-Val-OMe has been synthesized to investigate the effect of introduction of a strong beta-turn promoting guest segment into an oligopeptide with a tendency to form extended structures. 1H-nmr studies in solution using analysis of NH group solvent accessibility and nuclear Overhauser effects suggest an appreciable solvent dependence of conformations. In chloroform a 3(10)-helical structure is favored, while in dimethylsulfoxide an Aib-Pro beta-turn with extended arms on either side is suggested. In the crystal, the backbone forms a somewhat distorted 3(10)-helix despite the presence of a Pro residue in the middle. Among the four possible intrahelical hydrogen bonds three are of the 4----1 type and one 5----1. Head-to-tail NH...O = C hydrogen bonds link the helical molecules into continuous columns. The space group is P2(1)2(1)2(1) a = 11.320(2), b = 19.889(3), and c = 21.247(3) A.

Amino Acid Sequence↗

Sub-atomic resolution crystal structure of cholesterol oxidase: what atomic resolution crystallography reveals about enzyme mechanism and the role of the FAD cofactor in redox activity.

The crystal structure of cholesterol oxidase, a 56kDa flavoenzyme was anisotropically refined to 0.95A resolution. The final crystallographic R-factor and R(free) value is 11.0% and 13.2%, respectively. The quality of the electron density maps has enabled modeling of alternate conformations for 83 residues in the enzyme, many of which are located in the active site. The additional observed structural features were not apparent in the previous high-resolution structure (1.5A resolution) and have enabled the identification of a narrow tunnel leading directly to the isoalloxazine portion of the FAD prosthetic group. The hydrophobic nature of this narrow tunnel suggests it is the pathway for molecular oxygen to access the isoalloxazine group for the oxidative half reaction. Resolving the alternate conformations in the active site residues provides a model for the dynamics of substrate binding and a potential oxidation triggered gating mechanism involving access to the hydrophobic tunnel. This structure reveals that the NE2 atom of the active site histidine residue, H447, critical to the redox activity of this flavin oxidase, acts as a hydrogen bond donor rather than as hydrogen acceptor. The atomic resolution structure of cholesterol oxidase has revealed the presence of hydrogen atoms, dynamic aspects of the protein and how side-chain conformations are correlated with novel structural features such as the oxygen tunnel. This new structural information has provided us with the opportunity to re-analyze the roles played by specific residues in the mechanism of the enzyme.

Binding Sites↗

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.

Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP-ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding C(alpha) root mean square deviations (RMSD) of about 1.0 and 0.8 A respectively along the entire simulation time, compared to 0.8 A for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a C(alpha) RMSD of approximately 1.4 A, while the PAR22/LD trajectory became unstable early in the simulation, reaching a C(alpha) RMSD of about 2.7 A and remaining at this value until the end of the simulation; the C(alpha) RMSD of the EW/MD simulation was about 1.5 A. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35-ns SCP-ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (C(alpha) RMSD of approximately 1.0 A), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a C(alpha) RMSD of approximately 1.5 A at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent-exposed side chain-side chain (sc-sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation were lost. The overall analysis reported in this work suggests that the combination of an atomistic representation of a protein with a CMAP/CHARMM force field and a continuum representation of solvent effects such as the SCP-ISM provides a good description of structural and dynamic properties obtained from long computer simulations. Although the SCP-ISM simulations (CMAP/LD) reported here were shown to be stable and the properties well reproduced, further refinement is needed to attain a level of accuracy suitable for more challenging biological applications, particularly the study of protein-protein interactions.

Alanine↗

Trapping an activated conformation of mammalian carbamyl-phosphate synthetase.

The amidotransferase or glutaminase domain (GLN domain) of mammalian carbamyl-phosphate synthetase II (CPSase II) catalyzes glutamine hydrolysis and transfers ammonia to the synthetase domain (CPS domain), where carbamyl phosphate formation is catalyzed in three consecutive reactions. The GLN and CPS domains are part of a single polypeptide and are connected via a 29-amino acid chain segment (GC linker). In contrast, the two comparable domains of Escherichia coli CPSase are not fused, but are separate, noncovalently associated subunits. To establish the function of the GC linker in mammalian CPSase, it was deleted, and the two domains were directly fused. The deletion mutant not only catalyzed glutamine-dependent carbamyl phosphate synthesis, but was activated 10-fold relative to its wild-type counterpart. However, ammonia-dependent synthesis of carbamyl phosphate was abolished, indicating that ammonia no longer had access to the active site on the CPS domain. The mutant was still sensitive to inhibition by the allosteric effector UTP, but was no longer activated by the allosteric effector phosphoribosyl pyrophosphate, although evidence indicated that the latter could bind to the enzyme. The linker appears to serve as a spacer that allows the complex to cycle between two conformations, an open low activity form in which the ammonia site on the CPS domain is accessible and an activated conformation in which the ammonia generated in situ from glutamine is directly channeled to the CPS active site and access to exogenous ammonia is blocked.

Amino Acid Sequence↗

Role of subunit interfaces in the allosteric mechanism of hemoglobin.

We calculate the surface area buried in subunit interfaces of human deoxyhemoglobin and of horse methemoglobin. A larger surface area is buried in deoxy- than in methemoglobin as a result of tertiary and quaternary structure changes. In both molecules the dimer-dimer interface is closepacked. This implies that hydrophobicity stabilizes the deoxystructure, the free energy spent in keeping the subunits in a low-affinity conformation being compensated by hydrophobic free energy due to the smaller surface area accessible to solvent.

Allosteric Regulation↗

Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin.

Protein function is often regulated by conformational changes that occur in response to ligand binding or covalent modification such as phosphorylation. In many multidomain proteins these conformational changes involve reorientation of domains within the protein. Although X-ray crystallography can be used to determine the relative orientation of domains, the crystal-state conformation can reflect the effect of crystal packing forces and therefore may differ from the physiologically relevant form existing in solution. Here we demonstrate that the solution-state conformation of a multidomain protein can be obtained from its X-ray structure using an extensive set of dipolar couplings measured by triple-resonance multidimensional NMR spectroscopy in weakly aligning solvent. The solution-state conformation of the 370-residue maltodextrin-binding protein (MBP) loaded with beta-cyclodextrin has been determined on the basis of one-bond (15)N-H(N), (15)N-(13)C', (13)C(alpha)-(13)C', two-bond (13)C'-H(N), and three-bond (13)C(alpha)-H(N) dipolar couplings measured for 280, 262, 276, 262, and 276 residues, respectively. This conformation was generated by applying hinge rotations to various X-ray structures of MBP seeking to minimize the difference between the experimentally measured and calculated dipolar couplings. Consistent structures have been derived in this manner starting from four different crystal forms of MBP. The analysis has revealed substantial differences between the resulting solution-state conformation and its crystal-state counterpart (Protein Data Bank accession code 1DMB) with the solution structure characterized by an 11(+/-1) degrees domain closure. We have demonstrated that the precision achieved in these analyses is most likely limited by small uncertainties in the intradomain structure of the protein (ca 5 degrees uncertainty in orientation of internuclear vectors within domains). In addition, potential effects of interdomain motion have been considered using a number of different models and it was found that the structures derived on the basis of dipolar couplings accurately represent the effective average conformation of the protein.

Amino Acid Sequence↗

Activation for catalysis of penicillin-binding protein 2a from methicillin-resistant Staphylococcus aureus by bacterial cell wall.

Methicillin-resistant Staphylococcus aureus (MRSA) has acquired a unique penicillin-binding protein (PBP), PBP 2a, which has rendered the organism resistant to the action of all available beta-lactam antibiotics. The X-ray structure of PBP 2a shows the active site in a closed conformation, consistent with resistance to inhibition by beta-lactam antibiotics. However, it is known that PBP 2a avidly cross-links the S. aureus cell wall, which is its physiological function. It is shown herein that synthetic fragments of the bacterial cell wall bind in a saturable manner to PBP 2a and cause a conformational change in the protein that makes the active site more accessible to binding to a beta-lactam antibiotic. These observations and measurements point to a novel strategy by nature to keep the active site of PBP 2a sheltered from the inhibitory activity of the antibiotics, yet it becomes available to the polymeric cell wall by a requisite conformational change for the critical cell wall cross-linking reaction.

Catalysis↗

The structure of complement C3b provides insights into complement activation and regulation.

The human complement system is an important component of innate immunity. Complement-derived products mediate functions contributing to pathogen killing and elimination. However, inappropriate activation of the system contributes to the pathogenesis of immunological and inflammatory diseases. Complement component 3 (C3) occupies a central position because of the manifold biological activities of its activation fragments, including the major fragment, C3b, which anchors the assembly of convertases effecting C3 and C5 activation. C3 is converted to C3b by proteolysis of its anaphylatoxin domain, by either of two C3 convertases. This activates a stable thioester bond, leading to the covalent attachment of C3b to cell-surface or protein-surface hydroxyl groups through transesterification. The cleavage and activation of C3 exposes binding sites for factors B, H and I, properdin, decay accelerating factor (DAF, CD55), membrane cofactor protein (MCP, CD46), complement receptor 1 (CR1, CD35) and viral molecules such as vaccinia virus complement-control protein. C3b associates with these molecules in different configurations and forms complexes mediating the activation, amplification and regulation of the complement response. Structures of C3 and C3c, a fragment derived from the proteolysis of C3b, have revealed a domain configuration, including six macroglobulin domains (MG1-MG6; nomenclature follows ref. 5) arranged in a ring, termed the beta-ring. However, because neither C3 nor C3c is active in complement activation and regulation, questions about function can be answered only through direct observations on C3b. Here we present a structure of C3b that reveals a marked loss of secondary structure in the CUB (for 'complement C1r/C1s, Uegf, Bmp1') domain, which together with the resulting translocation of the thioester domain provides a molecular basis for conformational changes accompanying the conversion of C3 to C3b. The total conformational changes make many proposed ligand-binding sites more accessible and create a cavity that shields target peptide bonds from access by factor I. A covalently bound N-acetyl-l-threonine residue demonstrates the geometry of C3b attachment to surface hydroxyl groups.

Animals↗

The dynamic response of upstream DNA to transcription-generated torsional stress.

The torsional stress caused by counter-rotation of the transcription machinery and template generates supercoils in a closed topological domain, but has been presumed to be too short-lived to be significant in an open domain. This report shows that transcribing RNA polymerases dynamically sustain sufficient torsion to perturb DNA structure even on linear templates. Assays to capture and measure transcriptionally generated torque and to trap short-lived perturbations in DNA structure and conformation showed that the transient forces upstream of active promoters are large enough to drive the supercoil-sensitive far upstream element (FUSE) of the human c-myc into single-stranded DNA. An alternative non-B conformation of FUSE found in stably supercoiled DNA is not accessible dynamically. These results demonstrate that dynamic disturbance of DNA structure provides a real-time measure of ongoing genetic activity.

Base Sequence↗

Contribution of a buried aspartate residue towards the catalytic efficiency and structural stability of Bacillus stearothermophilus lactate dehydrogenase.

The X-ray structure of lactate dehydrogenase (LDH) shows the side-chain carboxylate group of Asp-143 to be buried in the hydrophobic interior of the enzyme, where it makes hydrogen-bonding interactions with both the side-chain hydroxyl group of Ser-273 and the main-chain amide group of His-195. This is an unusual environment for a carboxylate side-chain as hydrogen bonding normally occurs with water molecules at the surface of the protein. A charged hydrogen-bonding interaction in the interior of a protein would be expected to be much stronger than a similar interaction on the solvent-exposed exterior. In this respect the side-chain carboxylate group of Asp-143 appears to be important for maintaining tertiary structure by providing a common linkage point between three discontinuous elements of the secondary structure, alpha 1F, beta K and the beta-turn joining beta G and beta H. The contribution of the Asp-143 side-chain to the structure and function of Bacillus stearothermophilus LDH was assessed by creating a mutant enzyme containing Asn-143. The decreased thermal stability of both unactivated and fructose-1,6-diphosphate (Fru-1,6-P2)-activated forms of the mutant enzyme support a structural role for Asp-143. Furthermore, the difference in stability of the wild-type and mutant enzymes in guanidinium chloride suggested that the carboxylate group of Asp-143 contributes at least 22 kJ/mol to the conformational stability of the wild-type enzyme. However, there was no alteration in the amount of accessible tryptophan fluorescence in the mutant enzyme, indicating that the mutation caused a structural weakness rather than a gross conformational change. Comparison of the wild-type and mutant enzyme steady-state parameters for various 2-keto acid substrates showed the mutation to have a general effect on catalysis, with an average difference in binding energy of 11 kJ/mol for the transition-state complexes. The different effects of pH and Fru-1,6-P2 on the wild-type and mutant enzymes also confirmed a perturbation of the catalytic centre in the mutant enzyme. As the side-chain of Asp-143 is not sufficiently close to the active site to be directly involved in catalysis or substrate binding it is proposed that the effects on catalysis shown by the mutant enzyme are induced either by a structural change or by charge imbalance at the active site.(ABSTRACT TRUNCATED AT 400 WORDS)

Aspartic Acid↗

Identification of antigenic sites on the Na+/K(+)-ATPase beta-subunit: their sequences and the effects of thiol reduction upon their structure.

In contrast to the catalytic (alpha) subunit of the Na+/K(+)-ATPase holoenzyme, the glycoprotein (beta) subunit has proven to be a poor antigen for monoclonal antibody (Mab) production. However, in this work six Mabs directed against the beta-subunit of the lamb kidney holoenzyme have been isolated. These Mabs all recognize the holoenzyme, but their 'in solution' binding affinities for deglycosylated enzyme or isolated beta are generally at least 10-fold higher. Species specificity mapping, antibody patterns of binding to beta-fragments and competition binding studies indicated that there were only three distinct epitopes, with two antibodies binding in the NH2-terminal half (epitopes I and II) and 4 Mabs binding at the same or overlapping site (III) in the -COOH terminal half of beta. DNA sequence analysis of isolated collections of bacteriophage M13 that contain a 15 amino-acid 'epitope library' insert in the pIII protein, which enables them to bind to the antibodies, revealed the residues KYRDS (amino acids 111-115) and LETYP (amino acids 197-201) to be the deduced sequences for the epitopes of Mabs M19-P7-E5 (II) and M17-P5-F11 (III), respectively. The epitope I site was not, however, identified. Further studies showed that antibody binding to these three determinant sites had no affect on the Na+/K(+)-ATPase and K(+)-stimulated p-nitrophenylphosphatase (pNPPase) activities of either holoenzyme or deglycosylated enzyme, nor any affect on the cation- (Na+, K+ or Mg2+) and ouabain-induced conformational changes monitored with FITC-labeled deglycosylated enzyme. Interestingly, anti-beta Mab access to the three epitopes was increased following beta-mercaptoethanol inactivation of the holoenzyme, but this thiol reduction abolished the binding of two conformation-sensitive anti-alpha Mabs to the enzyme. These results are consistent with the previous suggestion of Kirley ((1990) J. Biol. Chem. 265, 4227-4232) that the beta-disulfide linkages not only maintain beta-structure but they are critical for maintaining alpha-conformation and holoenzyme activity.

Amino Acid Sequence↗