Complete unfolding of the titin molecule under external force

Titin (also known as connectin) is a giant filamentous protein that spans the distance between the Z- and M-lines of the vertebrate muscle sarcomere. Several earlier studies have implicated titin as playing a fundamental role in maintaining sarcomeric structural integrity and generating the passive force of muscle. The elastic properties of titin were characterized in recent single-molecule mechanical works that described the molecule as an entropic spring in which partial unfolding may take place at high forces during stretch and refolding at low forces during release. In the present work titin molecules were stretched using a laser tweezer with forces above 400 pN. The high external forces resulted in complete mechanical unfolding of the molecule, characterized by the disappearance of force hysteresis at high forces. Titin refolded following complete denaturation, as the hysteresis at low forces reappeared in subsequent stretch-release cycles. The broad force range throughout which unfolding occurred indicates that the various globular domains in titin require different unfolding forces due to differences in the activation energies for their unfolding.     

Reversible unfolding of the major fraction of ovalbumin by guanidine hydrochloride

The guanidine hydrochloride induced unfolding of the major fraction of ovalbumin (i.e. A1 which contains two phosphate groups and constitutes about 77% of the total protein) was investigated systematically by difference spectran and viscosity measurements. As judged by the intrinsic viscosity (3.9 ml/g), the native protein conformation is compact and globular. Difference spectral results showed extensive disruption of the native structure by guanidine hydrochloride with and without 0.1 M beta-mercaptoethanol were 31.1 and 27.0 ml/g. These and optical rotation results indicated that the denatured protein existed in a cross-linked random coil conformation in 6 M guanidine hydrochloride alone. Strikingly, in contrast to whole ovalbumin, the denaturation of its A1 fraction by guanidine hydrochloride was fully reversible and obeyed first-order kinetic law under different experimental condit ions of pH, temperature, and the denaturant concentration. The monotonic variation of deltaH for the unfolding of ovalbumin A1 by guanidine hydrochloride with temperature, the coincidence of the two transition curves obtained by measuring two independent properties (namely reduced viscosity and difference in light absorption at 288 nm (or 293 nm) as a function of the denaturant concentration, and finally the adherence of the unfolding as well as refolding reactions to first-order kinetic law suggested that the transition of ovalbumin. A1 can reasonably be approximated by a two-state mode. Analysis of the equilibrium data obtained at pH 7.0 and 25 degrees C according to Aune and Tanford (Aune, K.C.,and Tanford, C. (1969), Biochemistry 8, 4586) showed that 12 additional binding sites for the denaturant with an association constant of 1.12 were freshly exposed by the unfolding process and that the native protein was marginally more stable (approximately 6 kcal/mol) than its unfolded form even under native condition. The temperature dependence of the equilibrium constant for the unfolding of ovalbumin A1 by guanidine hydrochloride which was studied in the range 10-60 degrees C at pH 7.0 can be described by assigning the following values of the thermodynamic parameters for the unfolding process: deltaH = 52 kcal/mol at 25 degrees C; deltaS = 153 cal deg-1 mol-1 at 25 degrees C; and delta Cp = 2700 +/- 400 cal deg-1 mol-1.     

Reversible association of the equilibrium unfolding intermediate of lambda Cro repressor

An extended differentiated scanning calorimetry study of the wild-type Cro repressor and of its V55C mutant has revealed a significant concentration dependence of the melting profiles, even though the two polypeptide chains forming the active repressor molecule are covalently bound within the mutant. An analysis of the temperature dependencies of the partial molar heat capacity suggests that in both cases equilibrium unfolding occurs via a highly-populated intermediate state corresponding to polypeptide tetramers. The results of thermodynamic analysis are confirmed by direct glutaraldehyde cross-linking experiments. Judging by heat effects and circular dichroism data, this intermediate state regains about 50% of the ordered structure and melts co-operatively.     

Sequence profiles of immunoglobulin and immunoglobulin-like domains

Immunoglobulins (Ig) are highly modular proteins, consisting of variable and constant domains, which have clear, conserved sequence patterns. These sequence patterns have allowed T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule domains, as well as some cell adhesion, cell surface receptor and muscle protein domains, to be identified as forming a superfamily of related proteins together with the Ig-domains. The domains of these proteins have been grouped into four sets: variable (V-set), constant-1 (C1-set), constant-2 (C2-set) and intermediate (I-set). X-ray and NMR studies have shown that these domains form a Greek-key beta-sandwich structure with the sets differing in the number of strands in the beta-sheets as well as in their sequence patterns. The conserved sequence elements in the major sets of Ig and Ig-like molecules have previously been reported as general sequence profiles. This work examines the variability within these sets. Detailed sequence profiles and consensus sequences for these sets and groups have been constructed and a novel form of presentation has been developed to overcome some of the drawbacks of current methods of presenting consensus sequences. The profiles that were constructed allow a comparison of the similarities and differences among the sets of Ig and Ig-like sequences and provide a means by which sequences can be tested for compatibility with Ig-like sequence motifs. As well, the sequence separations of the main residues in the characteristic "pin" structure of Ig-like molecules were examined for variation among the groups. From the profiles constructed here, measures of the degree of conservation within the groups of molecules were determined. These measures were used to assist in a reconsideration of possible evolutionary pathways between the major structural groups of the Ig-superfamily.     

Recognition specificity of individual EH domains of mammals and yeast

The Eps homology (EH) domain is a recently described protein binding module that is found, in multiple or single copies, in several proteins in species as diverse as human and yeast. In this work, we have investigated the molecular details of recognition specificity mediated by this domain family by characterizing the peptide-binding preference of 11 different EH domains from mammal and yeast proteins. Ten of the eleven EH domains could bind at least some peptides containing an Asn-Pro-Phe (NPF) motif. By contrast, the first EH domain of End3p preferentially binds peptides containing an His-Thr/Ser-Phe (HT/SF) motif. Domains that have a low affinity for the majority of NPF peptides reveal some affinity for a third class of peptides that contains two consecutive amino acids with aromatic side chains (FW or WW). This is the case for the third EH domain of Eps15 and for the two N-terminal domains of YBL47c. The consensus sequences derived from the peptides selected from phage-displayed peptide libraries allows for grouping of EH domains into families that are characterized by different NPF-context preference. Finally, comparison of the primary sequence of EH domains with similar or divergent specificity identifies a residue at position +3 following a conserved tryptophan, whose chemical characteristics modulate binding preference.     

Modeling of anti-nucleosome immunoglobulin Fv domains: analysis of electrostatic interactions

Three-dimensional structural models of six murine anti-(H2A-H2B) monoclonal autoantibody variable fragments were built by comparative molecular modeling using the COMPOSER software. Analysis of the antibody combining sites is based on the hypothesis that ionic and/or electrostatic interactions predominate in antigen antibody binding, as suggested by the cationic nature of histones and the amino acid sequences of the antibody hypervariable regions. The study of the electrostatic potentials of their combining site surfaces, computed with the MOLCAD software, and the comparison with the electrostatic potentials of 13 selected control mAbs show the lack of a unique electrostatic pattern. One group of three mAbs expresses a strong and large electronegative area, supporting the hypothesis that ionic interactions predominate in antigen recognition. The second group, containing the other three mAbs, exhibits an alternation of electropositive and electronegative areas. All, however, present a localized electronegative area in the vicinity of H-CDR1 and H-CDR2 loops that is generated by the presence of at least one acidic residue. The model suggesting that the binding activity may depend on charged residues at the same site is reminiscent of what was previously reported in anti-DNA mAbs. In addition, the alternation of electropositive areas and electronegative areas in second group mAbs is also frequently observed in certain anti-DNA mAbs. These data argue for the existence of relationships between these two autoantibody populations and suggest that they share a common immunogenic particle formed by anionic and cationic components, such as a nucleosome.     

The three-dimensional structure of a type I module from titin: a prototype of intracellular fibronectin type III domains

BACKGROUND: Titin is a huge protein ( approximately 3 MDa) that is present in the contractile unit (sarcomere) of striated muscle and has a key role in muscle assembly and elasticity. Titin is mainly composed of two types of module (type I and II). Type I modules are found exclusively in the region of titin localised in the A band, where they are arranged in a super-repeat pattern that correlates with the ultrastructure of the thick filament. No structure of a titin type I module has been reported so far. RESULTS: We have determined the structure of a representative type I module, A71, using nuclear magnetic resonance (NMR) spectroscopy. The structure has the predicted fibronectin type III fold. Titin-specific conserved residues are either located at the putative module-module interfaces or along one side of the protein surface. Several proline residues that contribute to two stretches in a polyproline II helix conformation are solvent-exposed and line up as a continuous ribbon extending over more than two-thirds of the module surface. Homology models of the type I module N-terminal to A71 (A70) and the double module A70-A71 were used to discuss possible intermodule interactions and their role in module-module orientation. CONCLUSIONS: As residues at the module-module interfaces are highly conserved, we speculate that similar interactions govern all of the interfaces between type I modules in titin. This conservation would lead to a regular multiple array of similar surface structures. Such an arrangement would allow arrays of contiguous type I modules to expose multiple proline stretches in a highly regular way and these may act as binding sites for other thick filament proteins.     

Thymocyte development in the absence of pre-T cell receptor extracellular immunoglobulin domains

Immature thymocytes express a pre-T cell receptor (pre-TCR) composed of the TCRbeta chain paired with pre-Talpha. Signals from this receptor are essential for passage of thymocytes through a key developmental checkpoint in the thymus. These signals were efficiently delivered in vivo by a truncated form of the murine pre-TCR that lacked all of its extracellular immunoglobulin domains. De novo expression of the truncated pre-TCR or an intact alphabetaTCR was sufficient to activate characteristic TCR signaling pathways in a T cell line. These findings support the view that recognition of an extracellular ligand is not required for pre-TCR function.     

Vectors for the expression of PCR-amplified immunoglobulin variable domains with human constant regions

Cassette vectors have been constructed for mammalian expression of complete immunoglobulin heavy and light chain genes whose variable regions are produced by the polymerase chain reaction (PCR). The light and heavy chain vectors have promoter, leader, partial intron, enhancer and constant region segments within modified pSV2-gpt and pSV2-neo plasmids, respectively. Variable (V) regions are obtained by PCR using a two step process: 1) the V gene is amplified from genomic or cDNA, cloned into an intermediate vector and sequenced; 2) the first PCR product serves as the template for a second amplification in which restriction enzyme recognition sites and limited flanking intron sequence are added. The second PCR product is inserted into the expression vector, which is then transfected into mouse myeloma cells. These vectors contain human constant regions and may be used to express chimeric, humanized or human Ig genes. This report describes the design of these vectors and their application for the expression of chimeric 60.3, an anti-CD18 antibody.     

Sequencing and modeling of anti-DNA immunoglobulin Fv domains. Comparison with crystal structures

Models for the three-dimensional structures of the combining regions of six DNA-binding antibodies have been derived from the sequence data for their Fv domains presented here. Using the amino acid sequences and the canonical structure classes described by Chothia and Lesk (Chothia, C., and Lesk, A.M. (1987) J. Mol. Biol. 196, 901), model loops were selected from immunoglobulin domains of known structure for five of the six antibody hypervariable regions. Models for the third complementarity-determining region of the heavy chain were constructed from known immunoglobulin loops of similar length and sequence. Comparison of three of the models with the respective crystal structure indicates that this procedure can generate a working model of the antibody combining region that provides useful information on the nature of the interactions between antibodies and nucleic acids. As part of our continuing investigation into the structural basis of antibody-DNA recognition, the observed and predicted models for the combining regions of nucleic acid-binding antibodies have been examined. In general, single strand-specific antibodies have deep clefts where the antigen might bind, whereas duplex-specific antibodies present a relatively flat surface. In addition, on the basis of both sequence and structure, there is little to distinguish autoimmune antibodies from those produced by immunization. Testable hypotheses for how these antibodies might interact with single- and double-stranded nucleic acids are presented.     

Structure and function of immunoglobulin domains. V. Binding, University of immunoglobulin G and fragments to placental membrane preparations

Fc receptors have been shown to be present in human placental tissue with properties distinct from those on macrophages and lymphocytes. A single class of receptor was observed with an intrinsic affinity 4X 10(6) M-(1) for human IgG1. The order of affinity for IgG subclasses was IgG1 = IGG1 greater than IgG3 greater than IgG4. IgA and IgM were not bound. Fc from IgG1 bound with the same affinity as the whole molecule and to the same number of receptor sites, 2 X 10 (12)/mg placental protein. IgG1 was no longer boung after mild reduction and alkylation whereas the binding of Fc was unaffected by this treatment. Neithe C3 nor C3, the two domains which comprise the Fc region of IgG1, bound to the placental receptor. This implies that this Fc receptor is unlike those found on most cell surfaces and that plasental binding is an exception to the theory that each domain has evoked to perform independent functions.     

Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules

We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of structures. A geometrical core is defined as the set of residues such that the C alpha (I) - C alpha (J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units--strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures leads to the identification of two geometrical core sets of C alpha atom positions for the VL and VH domains. Applications of the core sets are described.     

Deterioration of connectin/titin and nebulin filaments by an excess of protease inhibitors

OBJECTIVE: To investigate HLA class II allele associations with autoantibody responses to Ro/SS-A and La/SS-B among Japanese subjects. METHODS: Haplotype and allele distributions, along with molecular polymorphisms, of HLA class II genes were analyzed by polymerase chain reaction-restriction fragment length polymorphism in 41 Japanese women with precipitating autoantibodies to Ro/SS-A and/or La/SS-B. RESULTS: Among women with both Ro/SS-A and La/SS-B antibodies, the HLA class II haplotype DRB1*08032/DQA1*0103/DQB1*0601 and DRB1*08032 allele showed significantly increased frequencies compared with patients with anti-Ro/SS-A alone or with normal controls. All women with both anti-Ro/SS-A and anti-La/SS-B, but not those with anti-Ro/SS-A alone, carried DRB1 alleles that shared the same amino acid residues at positions 14-31 and 71 of the hypervariable regions of the DRB1 chain. All anti-Ro/SS-A positive women carried 1 or 2 alleles of DQB1*06 and DQB1*03 subtypes that shared the same amino acid residues at positions 71-77 of the DQB1 chain. HLA class II allele distributions did not differ among 3 anti-Ro/SS-A positive groups with different disease expressions, i.e., patients with systemic lupus erythematosus, patients with primary Sj?gren's syndrome, and women with no apparent symptoms of rheumatic disease. CONCLUSION: HLA class II allele distributions differ among anti-Ro/SS-A positive subjects according to the presence or absence of coexisting anti-La/SS-B antibodies, but not according to disease expression. Our findings suggest that different HLA class II molecules might control the development of anti-Ro/SS-A and/or anti-La/SS-B antibodies in the autoimmune response to the Ro/SS-A-La/SS-B complex.     

Chimeric anti-TAG72 receptors with immunoglobulin constant Fc domains and gamma or zeta signalling chains

High serum levels of cholesterol and triglycerides are risk factors for coronary heart disease and are strongly related to several haemostatic parameters. Thyroid disorders are a frequent feature in hyperlipidemic patients and are also associated with a variety of haemostatic abnormalities. Therefore, we analysed the relationships between free T4 (fT4) levels and Factor VII and VIII activities (FVIIc and FVIIc), D-Dimers (DDI) and Plasminogen Activator Inhibitor type 1 (PAI-1), in a group of 472 healthy patients referred for hyperlipidemia. Fourty patients were found to have primary hypothyroidism. A negative correlation was found in the whole study population between fT4 and DDI (p = 0.0001, r = -0.21) and the same results were found after exclusion of the patients with fT4 below the normal range (p = 0.0007, r = -0.17). In a multivariate regression analysis, the relationship between DDI and fT4 was independent of age, Body Mass Index (BMI), gender and total cholesterol. Less impressive correlation coefficients were found with FVIIc (r = -0.10), FVIIIc (r = -0.09) and PAI-1 (r = -0.09). These results suggest that fT4 may play a physiological role in the regulation of the haemostatic equilibrium in hyperlipidemic patients and that low levels of fT4 are associated with a hypercoagulable state.     

Reversible denaturation of cyclosporin synthetase by urea

The reversible denaturation of the multifunctional polypeptide, cyclosporin synthetase, by urea was analyzed. It is possible to discriminate between at least two stages of enzyme denaturation. While at low urea concentration (up to 0.8M) cyclosporin A formation is inhibited, synthesis of the diketopiperazine cyclo-(D-alanyl-N-methylleucyl), a molecule representing a partial sequence of cyclosporin A is still detectable. At higher concentrations of urea the enzyme preparation is totally inactive. This inactivation is a consequence of conformational change(s) of cyclosporin synthetase as shown by fluorescence emission spectra of native and denatured enzyme. These data imply a consecutive folding/defolding mechanism for the different domains forming the multifuntional polypeptide.