Protein Folding and Protein Association

Membrane-assisted online renaturation for automated microfluidic lectin blotting

Aberrant glycosylation plays a pivotal role in a diverse set of diseases, including cancer. A microfluidic lectin blotting platform is introduced to enable and expedite the identification of protein glycosylation based on protein size and affinity for specific lectins. The integrated multistage assay eliminates manual intervention steps required for slab-gel lectin blotting, increases total assay throughput, limits reagent and sample consumption, and is completed using one instrument. The assay comprises non-reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) followed by online post-sizing SDS filtration and lectin-based affinity blotting. Important functionality is conferred through both device and assay advances that enable integration of nanoporous membranes flanking a central microchamber to create sub-nanoliter volume compartments that trap SDS-protein complexes and allow electrophoretic SDS removal with buffer exchange. Recapitulation of protein binding for lectin was optimized through quantitative assessment of SDS-treated green fluorescent protein. Immunoglobulin A1 aberrantly glycosylated with galactose-deficient O-glycans was probed in ~6 min using ~3 μL of sample. This new microfluidic lectin blotting platform provides a rapid and automated assay for the assessment of aberrant glycosylation.

Thermodynamic Analysis of the Dissociation of the Aldolase Tetramer Substituted at One or Both of the Subunit Interfaces

The fructose-1,6-bis(phosphate) aldolase isologous tetramer tightly associates through two different subunit interfaces defined by its 222 symmetry. Both single- and double-interfacial mutant aldolases have a destabilized quaternary structure, but there is little effect on the catalytic activity. These enzymes are however thermolabile. This study demonstrates the temperature-dependent dissociation of the mutant enzymes and determines the dissociation free energies of both mutant and native aldolase. Subunit dissociation is measured by sedimentation equilibrium in the analytical ultracentrifuge. At 25 degrees C the tetramer-dimer dissociation constants for each single-mutant enzyme are similar, about 10(-6) M. For the double-mutant enzyme, sedimentation velocity experiments on sucrose density gradients support a tetramer-monomer equilibrium. Furthermore, sedimentation equilibrium experiments determined a dissociation constant of 10(-15) M3 for the double-mutant enzyme. By the same methods the upper limit for the dissociation constant of wild-type aldolase A is approximately 10(-28) M3, which indicates an extremely stable tetramer. The thermodynamic values describing monomer-tetramer and dimer-tetramer equilibria are analyzed with regard to possible cooperative interaction between the two subunit interfaces.

Molecular chaperones--cellular machines for protein folding

Proteins are linear polymers synthesized by ribosomes from activated amino acids. The product of this biosynthetic process is a polypeptide chain, which has to adopt the unique three-dimensional structure required for its function in the cell. In 1972, Christian Anfinsen was awarded the Nobel Prize for Chemistry for showing that this folding process is autonomous in that it does not require any additional factors or input of energy. Based on in vitro experiments with purified proteins, it was suggested that the correct three-dimensional structure can form spontaneously in vivo once the newly synthesized protein leaves the ribosome. Furthermore, proteins were assumed to maintain their native conformation until they were degraded by specific enzymes. In the last decade this view of cellular protein folding has changed considerably. It has become clear that a complicated and sophisticated machinery of proteins exists which assists protein folding and allows the functional state of proteins to be maintained under conditions in which they would normally unfold and aggregate. These proteins are collectively called molecular chaperones, because, like their human counterparts, they prevent unwanted interactions between their immature clients. In this review, we discuss the principal features of this peculiar class of proteins, their structure-function relationships, and the underlying molecular mechanisms.

Conformational study and enantioselective, regiospecific syntheses of novel aminoxy trans-proline analogues derived from an acylnitroso Diels-Alder cycloaddition

The cis/trans isomerization of the proline amide bond has many implications in biological processes. The conformations of representative acylnitroso-derived proline analogues derived from cyclopentadiene were shown to exist exclusively as the E or trans conformation in CD2Cl2. The energetically favored conformations were determined using COSMO self-consistent reaction field calculations at the B3LYP/6-31G level of theory in addition to low temperature 1H NMR studies. The syntheses of the acylnitroso-derived peptides utilized two methods to selectively functionalize either of two chemically similar esters in the acylnitroso-derived amino acids. A novel transpeptidation of the amino acid that controlled the absolute stereochemistry in the acylnitroso Diels-Alder cycloaddition took advantage of an activated aminoxy amide linkage to control regiochemistry. Alternatively, an enantioselective and regiospecific enzymatic resolution of a racemic dimethyl ester provided a novel aminoxy acid.

Extending the concept of template-assembled synthetic proteins

The creation of native-like macromolecules in copying nature's way represents a fascinating challenge in protein chemistry today. In the absence of a detailed knowledge of the complex folding pathway the ultimate goal in protein de novo design, the construction of artificial proteins with predetermined three-dimensional structure and tailor-made functions based on a defined, generally valid set of rules, appears to be still out of reach. With progress in synthesis strategies and biostructural characterization methods, topological templates have become a versatile tool for inducing and stabilizing secondary and tertiary structures, such as protein loops, beta-turns, alpha-helices, beta-sheets and a variety of folding motifs. In this article, we extend the concept of template-assembled synthetic proteins for the construction of protein-like topologies with multiply bridged, oligocyclic chain architectures termed locked-in tertiary folds that exhibit unique physicochemical and folding properties because of the highly confined conformational space. Furthermore, we show that some fundamental questions in protein assembly can be approached applying the template concept. Using covalent template trapping of self-associated peptide assemblies in aqueous solution the structural and physical forces guiding protein folding, supramolecular assembly and molecular recognition processes can be studied on a molecular level.

Kinetic study on thermal denaturation of hen egg-white lysozyme involving precipitation

A kinetic study on the thermal denaturation accompanying precipitation of hen egg-white lysozyme was performed at temperatures between 50 and 90 degrees C. Visible precipitation occurred at lysozyme concentrations higher than 10(-5)M. Even at the concentration of 10(-6)M where no visible precipitation was observed, irreversible and reversible denaturation could be clearly discriminated. The former involves two different reactions with activation energies of approximately 93 and 50 kJ x mol(-1). On the other hand, enthalpy and entropy changes in the latter are 443 kJ x mol(-1) and 1280 J x K(-1) x mol(-1), respectively, indicating a large conformational change. The contradiction that the denaturation or deactivation reaction fitted first-order reaction kinetics while its rate constant depended on the protein concentration, was resolved by newly proposed schemes. The apparent first-order rate constant obtained experimentally depended on the initial protein concentration being on the order of almost unity. Moreover, it was revealed that the apparent first-order reaction involved a second-order reaction that characterized the aggregation of denatured protein molecules. The theory developed here explained reasonably the thermal denaturation accompanying precipitation that occurs at high protein concentration and at high temperature, and was also successfully applied to the lower concentration range with no accompanying precipitation.

Mutational effects on inclusion body formation in the periplasmic expression of the immunoglobulin VL domain REI

BACKGROUND

Inclusion body (IB) formation in bacteria is an important example of protein misassembly, a phenomenon which also includes folding-dependent aggregation in vitro and amyloid deposition in human disease. Previous studies of mutational effects in other systems implicate the stability of a folding intermediate-rather than the native state-as playing a key role in IB formation. To contribute to an understanding of the comparative biophysics of VL misassembly in different biological settings, we have studied mutation-dependent periplasmic IB formation by the VL domain REI in Escherichia coli.

RESULTS

A series of mutants were produced in periplasmic IBs, where, in all cases, the signal peptide was removed. In addition, the intradomain disulfide was clearly formed before deposition into IBs. IB formation in these mutants does not correlate with monomer/dimer equilibrium constants, but does correlate with the thermodynamic stability of the native state.

CONCLUSIONS

The results implicate a late, equilibrium folding intermediate in IB formation, in contrast to the apparent involvement of transient folding intermediates in other IB systems described to date. As equilibrium unfolding intermediates have also been implicated in light chain amyloidosis and deposition diseases, IB formation may prove a useful model for these human diseases.

Mutations and off-pathway aggregation of proteins

The off-pathway aggregation of proteins is a ubiquitous, yet poorly understood, phenomenon. In vitro, aggregation places limits on both protein stability and refolding yields. In vivo, it is responsible for inclusion-body formation in the bacterial production of proteins, as well as amyloid disease and related phenomena in animals. An important common feature of these processes is their sensitivity to point mutations, a feature that offers important clues for understanding controversial aspects of off-pathway aggregation such as its molecular specificity and the nature of the aggregating species. Results of a number of studies illustrate that the sensitivity of aggregation can derive from the ability of a mutation to either (1) facilitate the accumulation of a non-native state that is prone to aggregation, or (2) increase the intrinsic tendency of such a state to aggregate.

Inactive and temperature-sensitive folding mutants generated by tryptophan substitutions in the membrane-bound d-lactate dehydrogenase of Escherichia coli

A combination of site-specific mutagenesis and 19F nuclear magnetic resonance has been used to investigate the structural properties of D-lactate dehydrogenase, a membrane-associated enzyme of Escherichia coli. The protein (65,000 Da) has been labeled with 5-fluorotryptophan for 19F nuclear magnetic resonance studies. Tryptophan has been substituted for individual phenylalanine, tyrosine, isoleucine, and leucine residues at various positions throughout the enzyme molecule, and the fluorinated native and substituted tryptophan residues have been used as probes of the local environment. All 24 mutants thus generated are expressed in E. coli. Ten are fully active and purfiable following the usual procedure, while 14 either are inactive or produce low levels of activity. The amount of active enzyme produced from the low-yield mutants is dependent on the temperature at which synthesis is carried out, with more active enzyme produced at 18 degrees C than at 27, 35, or 42 degrees C. Cells grown at 27 degrees C and then incubated at 42 degrees C retain 90-100% of their activity. All of the expressed protein from the inactive mutants is Triton-insoluble, aggregated, and not readily purfiable; the inactive mutant protein appears to be improperly folded. Most of the expressed D-lactate dehydrogenase from the partially active mutants is also Triton-insoluble; a small fraction, however, is soluble in Triton and can be purified to yield active enzyme. All the purified enzymes from these low-yield mutants of D-lactate dehydrogenase have essentially normal VmaxS, and all but two have normal KmS. Once purified, the low-yield mutant enzymes are stable at 42 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)

Surface, subunit interfaces and interior of oligomeric proteins

The solvent-accessible surface area (As) of 23 oligomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. As is correlated with the protein molecular weight, and a power law predicts its value to within 5% on average. The accessible surface of the average oligomer is similar to that of monomeric proteins in its hydropathy and amino acid composition. The distribution of the 20 amino acid types between the protein surface and its interior is also the same as in monomers. Interfaces, i.e. surfaces involved in subunit contacts, differ from the rest of the subunit surface. They are enriched in hydrophobic side-chains, yet they contain a number of charged groups, especially from Arg residues, which are the most abundant residues at interfaces except for Leu. Buried Arg residues are involved in H-bonds between subunits. We counted H-bonds at interfaces and found that several have none, others have one H-bond per 200 A2 of interface area on average (1 A = 0.1 nm). A majority of interface H-bonds involve charged donor or acceptor groups, which should make their contribution to the free energy of dissociation significant, even when they are few. The smaller interfaces cover about 700 A2 of the subunit surface. The larger ones cover 3000 to 10,000 A2, up to 40% of the subunit surface area in catalase. The lower value corresponds to an estimate of the accessible surface area loss required for stabilizing subunit association through the hydrophobic effect alone. Oligomers with small interfaces have globular subunits with accessible surface areas similar to those of monomeric proteins. We suggest that these oligomers assemble from preformed monomers with little change in conformation. In oligomers with large interfaces, isolated subunits should be unstable given their excessively large accessible surface, and assembly is expected to require major structural changes.

Methods of molecular modelling of protein-protein interactions

This article reviews briefly theoretical methods attempting to predict the structure of protein aggregates from the structural features of their subunits. The authors discuss the problems of the solvent effect and the formation of protein structure. The existing methods of quaternary structure prediction are presented and an attempt at their classification is made at the end of this review.

Assembly of apoferritin from horse spleen: comparison of the protein in its native and reassembled state

The in vitro selfassembly of apoferritin after previous dissociation and unfolding in 7.2M guanidinium chloride, pH 3.5, yields up to 80% of a protein complex exhibiting the molecular mass of the native icositetramer of greater than or equal to 450 kDa. After removal of high molecular mass byproducts, the final reassembly product proves to be indistinguishable from native apoferritin with respect to its functional and conformational properties. These refer to the intrinsic fluorescence and to the far and near UV circular dichroism. The unfolding transitions of the native and reassembled protein in aqueous guanidinium chloride or at acid pH coincide within the range of error. The reassembled protein is also able to catalyze the oxidation of Fe(II). Higher polymers of the apoferritin complex represent most of the residual 20% of the reconstituted protein. They are stabilized by non-covalent (preferentially hydrophobic) interactions, and may be disassembled to the icositetramer by preferential solvation of the protein in the presence of less than or equal to 50% (v/v) ethylene glycol. The change in fluorescence emission accompanying polymerization reflects altered surface properties of the apoferritin subunits compatible with those reported for the ferritin----hemosiderin transition.

Proteolytic dimers of porcine muscle lactate dehydrogenase: characterization, folding, and reconstitution of the truncated and nicked polypeptide chain

Lactate dehydrogenase from porcine skeletal muscle is a "dimer of dimers" that is stabilized in its tetrameric state by an N-terminal "arm" of approximately 20 amino acid residues. Due to the low dissociation constant of the tetramer, the dimer is inaccessible to direct analysis. Limited proteolysis during reconstitution (after dissociation at pH 2.3) yields stable "dimers". As suggested by affinity chromatography, these inactive dimers contain the dinucleotide fold of native LDH. In the presence of structure-making ions, approximately 40% activity is restored in the dimeric state [Girg, R., Jaenicke, R., & Rudolph, R. (1983) Biochem. Int. 7, 443-444]. The cleavage yields about equal amounts of three fragments, F 34, F 21, and F 14 (Mr 33.5K, 21.4K, and 13.5K, respectively). F 34 represents the intact chain lacking the N-terminal 10-11 amino acid residues; its C-terminus is heterogeneous, varying in the range between residues 326 +/- 5. F 21 contains residues 11/12 to 200 +/- 3; F 14 is a mixture of three subfragments: residues 11/12 to approximately 133, 38 to approximately 163, and 208 to approximately 327. After solubilization in 6 M guanidine hydrochloride, F 34 can be reconstituted to partially active dimers. Reactivation is determined by slow subunit refolding with subsequent diffusion-controlled dimerization, in accordance with the monomer-dimer transition in the reconstitution mechanism of the intact tetramer. Reconstitution of F 21 and F 14 is concentration dependent and leads to partially active "nicked dimers", indicating that separate domains are able to reassociate correctly to yield the native subunit arrangement.

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

We assume that each class of protein has a core structure that is defined by internal residues, and that the external, solvent-contacting residues contribute to the stability of the structure, are of primary importance to function, but do not determine the architecture of the core portions of the polypeptide chain. An algorithm has been developed to supply a list of permitted sequences of internal residues compatible with a known core structure. This list is referred to as the tertiary template for that structure. In general the positions in the template are not sequentially adjacent and are distributed throughout the polypeptide chain. The template is derived using the fixed positions for the main-chain and beta-carbon atoms in the test structure and selected stereochemical rules. The focus of this paper is on the use of two packing criteria: avoidance of steric overlap and complete filling of available space. The program also notes potential polar group interactions and disulfide bonds as well as possible burial of formal charges. Central to the algorithm is the side-chain rotamer library. In an update of earlier studies by others, we show that 17 of the 20 amino acids (omitting Met, Lys and Arg) can be represented adequately by 67 side-chain rotamers. A list of chi angles and their standard deviations is given. The newer, high-resolution, refined structures in the Brookhaven Protein Data Bank show similar mean chi values, but have much smaller deviations than those of earlier studies. This suggests that a rotamer library may be a better structural approximation than was previously thought. In using packing constraints, it has been found essential to include all hydrogen atoms specifically. The "unified atom" representation is not adequate. The permitted rotamer sequences are severely restricted by the main-chain plus beta-carbon atoms of the test structure. Further restriction is introduced if the full set of atoms of the external residues are held fixed, the full-chain model. The space-filling requirement has a major role in restricting the template lists. The preliminary tests reported here make it appear likely that templates prepared from the currently known core structures will be able to discriminate between these structures. The templates should thus be useful in deciding whether a sequence of unknown tertiary structure fits any of the known core classes and, if a fit is found, how the sequence should be aligned in three dimensions to fit the core of that class.(ABSTRACT TRUNCATED AT 400 WORDS)

Reassociation of dimeric cytoplasmic malate dehydrogenase is determined by slow and very slow folding reactions

Malate dehydrogenase occurs in virtually all eucaryotic cells in mitochondrial and cytoplasmic forms, both of which are composed of two identical subunits. The reactivation of the mitochondrial isoenzyme has been the subject of previous studies [Jaenicke, R., Rudolph, R., & Heider, I. (1979) Biochemistry 18, 1217-1223]. In the present study, the reconstitution of cytoplasmic malate dehydrogenase from porcine heart after denaturation by guanidine hydrochloride has been determined. The enzyme is denatured by greater than 1.2 M guanidine hydrochloride; upon reconstitution, approximately 60% of the initial native enzyme can be recovered. The kinetics of reconstitution after maximum unfolding by 6 M guanidine hydrochloride were analyzed by fluorescence, far-ultraviolet circular dichroism, chemical cross-linking with glutaraldehyde, and activity measurements. After fast folding into structured intermediates (less than 1 min), formation of native enzyme is governed by two parallel slow and very slow first-order folding reactions (k1 = 1.3 X 10(-3) S-1 and k2 = 7 X 10(-5) S-1 at 20 degrees C). The rate constant of the association step following the slow folding reaction (determined by k1) must be greater than 10(6) M-1 S-1. The energy of activation of the slow folding step is of the order of 9 +/- 1 kcal/mol; the apparent rate constant of the parallel very slow folding reaction is virtually temperature independent. The intermediates of reassociation must be enzymatically inactive, since reactivation strictly parallels the formation of native dimers. Upon acid dissociation (pH 2.3), approximately 35% of the native helicity is preserved, as determined by circular dichroism.(ABSTRACT TRUNCATED AT 250 WORDS)

The versatility of proteolytic enzymes

The growing realization of their physiological importance has generated renewed interest in the study of proteolytic enzymes. Modern methods of protein chemistry and molecular biology have revealed new insights into the protein and gene structure of a variety of protein precursors and their processing by limited proteolysis. Examples are given in this review for transmembrane processes and the role of signal peptidases of both eukaryotic and prokaryotic origin, the processing of prohormones and precursors of growth factors, protein components of blood coagulation, fibrinolysis, and of the complement system, and a group of granulocyte proteases, including the mast cell serine proteases. The relationship of homologous domains found in many of these proteases and their zymogens to protein evolution is a recurrent theme of this discussion.

Evidence for active intermediates during the reconstitution of yeast phosphoglycerate mutase

The reconstitution of the tetrameric phosphoglycerate mutase from bakers' yeast after denaturation in guanidine hydrochloride has been studied. When assays are performed in the presence of trypsin, it is found that reactivation parallels the regain of tetrameric structure. However, in the absence of trypsin, the regain of activity is more rapid, suggesting that monomeric and dimeric intermediates possess partial activity (35% of the value of native enzyme) which is sensitive to trypsin. When reconstitution is studied in the presence of substrates, it is again found that monomeric and dimeric intermediates possess 35% activity. Under these latter conditions, the activity of the monomer but not of the dimer is sensitive to trypsin.