Biomedical subjects

R Jaenicke

Publications and source records attributed to R Jaenicke.

At least 109 records · Page 6Linked to original sources

PubMed1994

Design, creation, and characterization of a stable, monomeric triosephosphate isomerase.

Protein engineering on trypanosomal triosephosphate isomerase (TIM) converted this oligomeric enzyme into a stable, monomeric protein that is enzymatically active. Wild-type TIM consists of two identical subunits that form a very tight dimer involving interactions of 32 residues of each subunit. By replacing 15 residues of the major interface loop by another 8-residue fragment, a variant was constructed that is a stable and monomeric protein with TIM activity. The length, sequence, and conformation of the designed fragment were suggested by extensive modeling.

Amino Acid Sequence↗

PubMed1994

Domain interactions and connecting peptides in lens crystallins.

beta B2- and gamma B-crystallin from bovine eye-lens are closely related proteins, topologically distinct mainly by virtue of the linker peptide connecting the two domains in each polypeptide chain. In homodimeric beta B2-crystallin, the extended conformation of the connecting peptide has been suggested to force the beta B2-molecule to favor intermolecular domain interactions compared with intramolecular contacts in monomeric gamma B-crystallin. From this one may postulate that the conserved interdomain contacts are essential for the overall stability of crystallins. This was clearly confirmed for gamma B-crystallin, since its isolated C-terminal domain is significantly less stable than in the context of native gamma B. Exchanging the linker peptide of gamma B- for that of beta B2-crystallin yields a monomeric protein with stability characteristics identical to gamma B-crystallin. We conclude that the domain-interface itself rather than the connecting peptide determines the mode of domain association in crystallins, as the linker in the gamma B beta-mutant is evidently twisted to a turn similar to the one in natural gamma B-crystallin.

Amino Acid Sequence↗

PubMed1994

Response of bacteria and fungi to high-pressure stress as investigated by two-dimensional polyacrylamide gel electrophoresis.

In an attempt to generalize previous observations (Jaenicke et al., Appl. Environ. Microbiol. 1988, 54, 2375-2380) and to find a convenient model system for studies of the pressure response, we tested the suitability of Escherichia coli and Thermotoga maritima (bacteria), and of five different eukaryotic species including the filamentous fungi Asteromyces cruciatus and Dendryphiella salina, and the marine yeasts Debaryomyces hansenii, Rhodosporidium sphaerocarpum, and Rhodotorula rubra. Using two-dimensional polyacrylamide gel electrophoresis, detailed investigations on the pressure response were carried out with E. coli and Rhodosporidium sphaerocarpum. In the former organism, major pressure response proteins could not be detected, although there are significant differences in expression of some proteins as well as some minor components that are found in all of the high pressure cell extracts but not in extracts from cultures grown at atmospheric pressure. In Rhodosporidium sphaerocarpum, no change in protein expression patterns was observed between 0.1 and 20 MPa. However, approaching the limit of viability of 50 MPa, additional protein spots became detectable at 45 MPa. This finding correlates with the observation of abnormal growth forms of the organism at this pressure (Lorenz, R. et al. manuscript in preparation).

Bacterial Proteins↗

PubMed1994

Autonomous folding of the excised coenzyme-binding domain of D-glyceraldehyde 3-phosphate dehydrogenase from Thermotoga maritima.

An important question in protein folding is whether compact substructures or domains are autonomous units of folding and assembly. The protomer of the tetrameric D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima has a complex coenzyme-binding domain, in which residues 1-146 form a compact substructure with the last 31 residues (313-333). Here it is shown that the gene of a single-chain protein can be expressed in Escherichia coli after deleting the 163 codons corresponding to the interspersed catalytic domain (150-312). The purified gene product is a soluble, monomeric protein that binds both NAD+ and NADH strongly and possesses the same unfolding transition induced by guanidinium chloride as the native tetramer. The autonomous folding of the coenzyme-binding domain has interesting implications for the folding, assembly, function, and evolution of the native enzyme.

Amino Acid Sequence↗

PubMed1994

Dimerization of beta B2-crystallin: the role of the linker peptide and the N- and C-terminal extensions.

beta B2- and gamma B-crystallins of vertebrate eye lens are 2-domain proteins in which each domain consists of 2 Greek key motifs connected by a linker peptide. Although the folding topologies of beta B2- and gamma B-domains are very similar, gamma B-crystallin is always monomeric, whereas beta B2-crystallin associates to homodimers. It has been suggested that the linker or the protruding N- and C-terminal arms of beta B2-crystallin (not present in gamma B) are a necessary requirement for this association. In order to investigate the role of these segments for dimerization, we constructed two beta B2 mutants. In the first mutant, the linker peptide was replaced with the one from gamma B (beta B2 gamma L). In the second mutant, the N- and C-terminal arms of 15- and 12-residues length were deleted (beta B2 delta NC). The beta B2 gamma L mutant is monomeric, whereas the beta B2 delta NC mutant forms dimers and tetramers that cannot be interconverted without denaturation. The spectral properties of the beta B2 mutants, as well as their stabilities against denaturants, resemble those of wild-type beta B2-crystallin, thus indicating that the overall peptide fold of the subunits is not changed significantly. We conclude that the peptide linker in beta B2-crystallin is necessary for dimerization, whereas the N- and C-terminal arms appear to be involved in preventing the formation of higher homo-oligomers.

Amino Acid Sequence↗

PubMed1994

Three-dimensional model and quaternary structure of the human eye lens protein gamma S-crystallin based on beta- and gamma-crystallin X-ray coordinates and ultracentrifugation.

A 3-dimensional model of the human eye lens protein gamma S-crystallin has been constructed using comparative modeling approaches encoded in the program COMPOSER on the basis of the 3-dimensional structure of gamma-crystallin and beta-crystallin. The model is biased toward the monomeric gamma B-crystallin, which is more similar in sequence. Bovine gamma S-crystallin was shown to be monomeric by analytical ultracentrifugation without any tendency to form assemblies up to concentrations in the millimolar range. The connecting peptide between domains was therefore built assuming an intramolecular association as in the monomeric gamma-crystallins. Because the linker has 1 extra residue compared with gamma B and beta B2, the conformation of the connecting peptide was constructed by using a fragment from a protein database. gamma S-crystallin differs from gamma B-crystallin mainly in the interface region between domains. The charged residues are generally paired, although in a different way from both beta- and gamma-crystallins, and may contribute to the different roles of these proteins in the lens.

Amino Acid Sequence↗

PubMed1994

Eye-lens proteins: structure, superstructure, stability, genetics.

The eye lens in vertebrates and invertebrates is an avascular tissue which allows one to focus objects on the retina. The lens grows throughout life, maintaining transparency without significant turnover of its densely packed proteins. Apart from cytoskeletal and taxon-specific components, these proteins belong mainly to the alpha- and beta gamma-crystallin families. The detailed structural analysis of beta gamma-crystallins can explain the anomalous stability by the specific supersecondary structure ("Greek key" topology) of the domains and by strong domain and subunit interactions. The spatial correlation of the molecules at the given high concentrations in the fiber cells gives rise to "short-range order" with minimum light scattering, thus providing optimum transparency of the eye lens.

Animals↗

PubMed1994

N-ethylmaleimide-sensitive fusion protein: a trimeric ATPase whose hydrolysis of ATP is required for membrane fusion.

The NEM-sensitive fusion protein, NSF, together with SNAPs (soluble NSF attachment proteins) and the SNAREs (SNAP receptors), is thought to be generally used for the fusion of transport vesicles to their target membranes. NSF is a homotrimer whose polypeptide subunits are made up of three distinct domains: an amino-terminal domain (N) and two homologous ATP-binding domains (D1 and D2). Mutants of NSF were produced in which either the order or composition of the three domains were altered. These mutants could not support intra-Golgi transport, but they indicated that the D2 domain was required for trimerization of the NSF subunits. Mutations of the first ATP-binding site that affected either the binding (K266A) or hydrolysis (E329Q) of ATP completely eliminated NSF activity. The hydrolysis mutant was an effective, reversible inhibitor of Golgi transport with an IC50 of 125 ng/50 microliters assay. Mutants in the second ATP-binding site (binding, K549A; hydrolysis, D604Q) had either 14 or 42% the specific activity of the wild-type protein, respectively. Using coexpression of an inactive mutant with wild-type subunits, it was possible to produce a recombinant form of trimeric NSF that contained a mixture of subunits. The mixed NSF trimers were inactive, even when only one mutant subunit was present, suggesting that NSF action requires each of the three subunits in a concerted mechanism. These studies demonstrate that the ability of the D1 domain to hydrolyze ATP is required for NSF activity and, therefore is required for membrane fusion. The D2 domain is required for trimerization, but its ability to hydrolyze ATP is not absolutely required for NSF function.

Adenosine Triphosphatases↗

PubMed1994

The effect of ion pairs on the thermal stability of D-glyceraldehyde 3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima.

D-Glyceraldehyde 3-phosphate dehydrogenase from Thermotoga maritima (TmGAPDH) is intrinsically thermostable, exhibiting a thermal transition beyond 105 degrees C. Neither the amino-acid composition nor homology modelling, based on sequence alignment and known 3-D structures of the enzyme from meso- and thermophiles, provide an explanation of the anomalous stability. Recent X-ray data suggest that an increased number of ion pairs is involved. To prove this hypothesis, a number of charged residues contributing to ion pairs in TmGAPDH, but absent in the moderately thermophilic enzyme were altered. Elimination of peripheral ion pairs (E103-K104, E261-R266) was found to be ineffective. Altering a central charge cluster (R10-D47, E314, D*186) led to a drastic decrease in coenzyme binding. As a consequence, guanidine-dependent deactivation is shifted to significantly lower guanidinium chloride (GdmCl) concentrations without altering the denaturation/dissociation profile of the wild type enzyme. Mutants in the S loop (R195D, R195D-D181K) lead to a biphasic profile in the GdmCl-dependent denaturation transition and significant destabilization; at room temperature no subunit dissociation could be observed.

Amino Acid Sequence↗

PubMed1994

A structure-based model for the halophilic adaptation of dihydrofolate reductase from Halobacterium volcanii.

'Halophilic adaptation' of proteins, i.e. the requirement for high concentrations of monovalent ions for thermodynamic stability of proteins from halophilic organisms, is not fully understood. In this work, an explanation for the halophilic behavior of dihydrofolate reductase (h-DHFR) from Halobacterium volcanii is attempted, based on a model structure derived from comparative modeling to dihydrofolate reductase from Escherichia coli. The model structure of h-DHFR shows an unique asymmetrical charge distribution over the protein surface, with positively charged amino acids centered around the active site and negative charges on the opposite side of the enzyme. This particular charge distribution and the correlated molecular dipole are functionally relevant. The negative charges on the surface form clusters which are shielded at high salt concentrations; at low salt, they repulse each other, thus destabilizing the protein. Results are in accordance with denaturation data and, thus, provide an explanation for the exceptional stability properties of h-DHFR.

Amino Acid Sequence↗

PubMed1994

Relevance of sequence statistics for the properties of extremophilic proteins.

The amino acid composition of proteins from mesophilic and extremophilic organisms is commonly assumed to reflect the mechanisms of molecular adaptation to extremes of physical conditions. In this context, halophilic behaviour has been attributed to significantly increased numbers of aspartic and glutamic acid residues. However, extending the analysis to a statistically relevant set of related proteins, dihydrofolate reductase from Halobacterium volcanii, as an example, shows that the increase in negative charge is found to be less significant than other exchanges of amino acids (e.g., Ala, Asn, Arg, Lys, Phe, Ser). Thus, the high water binding capacity of negatively charged residues cannot be unambiguously correlated with the anomalous stability of halophilic proteins. A similar caveat holds for generalizations regarding the thermal stability of proteins. In this case, D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima was compared with a number of mesophilic and moderately thermophilic homologs. Again, 'traffic rules of stabilization', in terms of amino acid changes in going from mesophilic to thermophilic proteins, cannot be given.

Amino Acids↗

PubMed1993

The structures of native phosphorylated chicken cystatin and of a recombinant unphosphorylated variant in solution.

The solution structures of the phosphorylated form of native chicken cystatin and the recombinant variant AEF-S1M-M29I-M89L were determined by 2D, 3D and 4D-NMR. The structures turn out to be very similar, despite the substitutions and the phosphorylation of the wild-type. Their dominant feature is a five-stranded beta-sheet, which is wrapped around a five-turn alpha-helix, as shown by X-ray crystallographic studies of wild-type chicken cystatin. However, the NMR analysis shows that the second helix observed in the crystal is not present in solution. The phosphorylation occurs at S80, which is located in a flexible region. For this reason, very few effects on the structure are observed. Comparison of structures of the unphosphorylated variant and the wild-type shows small effects on H84 which is located in the supposed recognition site of the serine kinase. This recognition site appears to be well structured as a large loop-containing bulge of the beta-sheet. The N termini of both mutants, which contribute to a large extent to the binding to the proteinase, are very flexible. A loop structure involving the residues L7 to A10 as found in related inhibitors, such as in the kininogen domains 2 and 3, is not sufficiently populated to be observed.

Amino Acid Sequence↗

PubMed1993

Pressure-induced dissociation of ribosomes and elongation cycle intermediates. Stabilizing conditions and identification of the most sensitive functional state.

Pressure-induced dissociation of ribosomes has been considered a major reason for the inhibition of protein biosynthesis and, hence, bacterial growth at high hydrostatic pressure [Jaenicke, R. (1981) Annu. Rev. Biophys. Bioeng. 10, 1-67]. We reexamined the issue, using a buffer system with polyamines that has been optimized to reproduce in-vivo-like performance of protein biosynthesis in vitro. By slightly modifying this buffer, we were able to find conditions that stabilize functional ribosomal complexes against the dissociating effect of pressure up to 100 MPa and uncharged tight couples up to 60 MPa. Approaching the physiological conditions by reducing the Mg2+ concentration down to 4 mM, one finds a significant destabilization of the post-translocational complex, which represents the most pressure-sensitive intermediate of the elongation cycle and is possibly the limiting factor for the pressure-induced block of protein biosynthesis and bacterial growth.

Buffers↗

PubMed1993

The redox properties of protein disulfide isomerase (DsbA) of Escherichia coli result from a tense conformation of its oxidized form.

Periplasmic protein disulfide isomerase (DsbA) from Escherichia coli is a strongly oxidizing thiol reagent with one catalytic disulfide bridge and an intrinsic redox potential of -0.089 V. Gel filtration experiments and analytical ultracentrifugation studies demonstrate that DsbA is a monomeric protein with a molecular mass of 21.1 kDa, independent of its redox state. In order to investigate the molecular basis of its redox properties, the guanidinium.chloride-induced folding/unfolding equilibrium of the reduced and the oxidized form of the enzyme were compared. The transitions at pH 7.0 and 30 degrees C were found to be fully reversible and allowed the calculation of the free energy of stabilization of oxidized and reduced DsbA according to a two-state model for the unfolding transition. The analysis reveals that reduced DsbA is 22.7 (+/- 4.0) kJ/mol more stable than oxidized DsbA. This energetic difference is essentially independent of temperature, although the overall free energies of stabilization of both oxidized and reduced DsbA vary strongly between 20 and 30 degrees C as a consequence of changes in the cooperativity of the transitions The conformational tension of 22.7 (+/- 4.0) kJ/mol in oxidized DsbA quantitatively explains the oxidizing properties of the protein, as it causes a change of redox equilibrium constants between DsbA and thiols of about four orders of magnitude, corresponding to an increase of the standard redox potential of 0.118 (+/- 0.021) V. We conclude that the oxidizing properties of DsbA mainly result from a tense conformation of its oxidized form, that is converted to the relaxed, reduced state upon oxidation of thiols by DsbA. The results are discussed in terms of a general principle underlying the oxidizing properties of protein disulfide isomerases.

Chromatography, Gel↗

PubMed1993

Cloning, site-specific mutagenesis, expression and characterization of full-length chloroplast NADP-malate dehydrogenase from Pisum sativum.

Chloroplast NADP-dependent malate dehydrogenase is regulated by a dithiol redox reaction. The assignment of the groups involved, requires the primary structure of the enzyme to be known. Using the polymerase chain reaction and the cDNA library of Pisum sativum, the sequence of the enzyme and its targeting signal was determined. The gene was cloned in Escherichia coli JM83 and expressed in E. coli JM83 and E. coli B at high yield. The determination of the physical properties of the gene product proves the recombinant protein to be indistinguishable from the enzyme purified from the plant. This holds true, in spite of the fact that the plant enzyme lacks 11 N-terminal residues. The lengths of the complete polypeptide chain of the recombinant enzyme and its transit peptide are 388 and 53 residues, respectively. The comparison of the sequences of the mature enzyme with those of known chloroplast NADP-MDH shows 83-95% identity, but with mitochondrial or bacterial MDH only approximately 20%. Reduction of the (inactive) oxidized enzyme with dithiothreitol allows mimicking of the in vivo activation. The reaction follows a consecutive second-order-kinetics mechanism. Guanidinium chloride (GdmCl) at concentrations below 0.4 M leads to a significant activation of the oxidized form of the enzyme. At [GdmCl] = 0.4-0.46 M, both oxidized and reduced NADP-MDH show highly cooperative changes in the hydrodynamic and spectral properties, indicating the synchronous breakdown of the quaternary, tertiary and secondary structures. Site-directed mutations C23A and C28A do not quench the regulatory properties of the enzyme; additional substitution of alanine for Cys206 and Cys376 renders the enzyme equally active in both the reduced and the oxidized state. Therefore, one can consider these residues, either alone or in combination with Cys23 and Cys28, as responsible for enzyme activation.

Amino Acid Sequence↗

PubMed1993

The L-lactate dehydrogenase gene of the hyperthermophilic bacterium Thermotoga maritima cloned by complementation in Escherichia coli.

The gene for a L(+)-lactate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima was cloned by complementation of an Escherichia coli pfl. Idh mutant. The gene is part of a 4.5 kb SauIIIA fragment obtained by partial digestion of the Thermotoga genome. The DNA fragment was physically mapped and the putative Shine-Dalgarno sequence within the non-coding region determined. The gene contains 960 bp, including the stop codon, corresponding to 319 amino acids/subunit of the homotetrameric enzyme. Part of the amino acid sequence was confirmed by Edman degradation of peptides obtained from nanomolar quantities of the purified enzyme by tryptic digestion. A comparison of the amino acid sequence with those of known prokaryotic L-lactate dehydrogenases reveals a high similarity, especially with the enzyme from thermophilic sources, where up to 48% identity is found. The gene was expressed as an active enzyme in a heterologous host.

Amino Acid Sequence↗

PubMed1993

Functional expression of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima in Escherichia coli. Authenticity and kinetic properties of the recombinant enzyme.

The gene coding for D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima has been cloned and functionally expressed in Escherichia coli. Some 90% of the coding gene was amplified by the polymerase chain reaction. The amplified gene segment was in full agreement with the previously determined amino acid sequence [Schultes, V., Deutzmann, R., Jaenicke, R. (1990) Eur. J. Biochem. 192, 25-31] and was completed by the insertion of synthetic linkers using site-directed mutagenesis. The resulting semisynthetic gene was expressed in high yield in the cytoplasm of E. coli and the recombinant enzyme was purified to homogeneity. It was shown to be identical with the enzyme isolated directly from T. maritima in all enzymatic and physicochemical properties investigated. The enzyme is allosterically inhibited by both D- and L-glyceraldehyde 3-phosphate at concentrations above 1 mM, and by arsenate at concentrations above 10 mM. The expressed protein restores the natural E. coli phenotype in a gap- strain, thus providing evidence that the hyperthermophilic protein can fold and associate to its native, functional state in its mesophilic host.

Amino Acid Sequence↗

PubMed1993

Creatinase in its collapsed A state shows properties of a molten globule with dimeric quaternary structure.

In the past, the molten globule state at acidic pH (A state) has mainly been observed for small single-domain proteins. For more complex proteins such as immunoglobulin, alternatively folded states, with certain characteristics of the molten globule but different thermodynamic properties, were observed. In the present work, the acid-induced structural characteristics of a homodimer, creatinase from Pseudomonas putida, are described. The 91-kDa protein at pH 2 shows molten globule behavior in that there is (a) a high content of native-like secondary structure (monitored by far-ultraviolet circular dichroism), (b) changes in the solvent accessibility of intrinsic fluorophores (acrylamide quenching of protein fluorescence), (c) increased hydrophobic surface area (indicated by anomalous dye binding) and (d) a slight expansion of the hydrodynamic volume (calculated from S20,solv, obtained from analytical ultracentrifugation). The enzyme at pH 2 shows reversible cooperative transitions in guanidinium chloride or urea (at elevated ionic strength). Its quaternary structure remains unaltered, indicating that native-like subunit interactions are involved in the stabilization of the A state of the enzyme. Anions stabilize the compact conformation due to reduced intramolecular charge repulsion; for the same reason, the enzyme in its A state shows a strong tendency to aggregate at > 0.3 M NaCl.

Enzyme Stability↗