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Mice expressing only covalent dimeric heparin binding-deficient lipoprotein lipase: muscles inefficiently secrete dimeric enzyme.

Lipoprotein lipase (LpL) hydrolyzes triglycerides of circulating lipoproteins while bound as homodimers to endothelial cell surface heparan sulfate proteoglycans. This primarily occurs in the capillary beds of muscle and adipose tissue. By creating a mouse line that expresses covalent dimers of heparin-binding deficient LpL (hLpLHBM-Dimer) in muscle, we confirmed in vivo that linking two LpL monomers in a head to tail configuration creates a functional LpL. The hLpLHBM-Dimer transgene produced abundant activity and protein in muscle, and the LpL was the expected size of a dimer (approximately 110 kDa). Unlike the heparin-binding mutant monomer, hLpLHBM-Dimer had the same stability as nonmutated LpL. The hLpLHBM-Dimer transgene prevented the neonatal demise of LpL knockout mice; however, these mice were hypertriglyceridemic. Postheparin plasma LpL activity was lower than expected with the robust expression in muscle and was no longer covalently linked. Studies in transfected cells showed that Chinese hamster lung cells, but not COS cells, also degraded tandem repeated LpL into monomers. Thus, although muscle can synthesize tethered, dimeric LpL, efficient production of this enzyme leading to secretion, and physiological function appears to favor secretion of a noncovalent dimer composed of monomeric subunits.

Amino Acid Sequence↗

Crystal structure of the biglycan dimer and evidence that dimerization is essential for folding and stability of class I small leucine-rich repeat proteoglycans.

Biglycan and decorin are two closely related proteoglycans whose protein cores contain leucine-rich repeats flanked by disulfides. We have previously shown that decorin is dimeric both in solution and in crystal structures. In this study we determined whether biglycan dimerizes and investigated the role of dimerization in the folding and stability of these proteoglycans. We used light scattering to show that biglycan is dimeric in solution and solved the crystal structure of the glycoprotein core of biglycan at 3.40-angstroms resolution. This structure reveals that biglycan dimerizes in the same way as decorin, i.e. by apposition of the concave inner surfaces of the leucine-rich repeat domains. We demonstrate that low concentrations of guanidinium chloride denature biglycan and decorin but that the denaturation is completely reversible following removal of the guanidinium chloride, as assessed by circular dichroism spectroscopy. Furthermore, the rate of refolding is dependent on protein concentration, demonstrating that it is not a unimolecular process. Upon heating, decorin shows a single structural transition at a T(m) of 45-46 degrees C but refolds completely upon cooling to 25 degrees C. This property of decorin enabled us to show both by calorimetry and light scattering that dimer to monomer transition coincided with unfolding and monomer to dimer transition coincided with refolding; thus these processes are inextricably linked. We further conclude that folded monomeric biglycan or decorin cannot exist in solution. This implies novel interrelated functions for the parallel beta sheet faces of these leucine-rich repeat proteoglycans, including dimerization and stabilization of protein folding.

Amino Acid Sequence↗

Residue R113 is essential for PhoP dimerization and function: a residue buried in the asymmetric PhoP dimer interface determined in the PhoPN three-dimensional crystal structure.

Bacillus subtilis PhoP is a member of the OmpR/PhoB family of response regulators that is directly required for transcriptional activation or repression of Pho regulon genes in conditions under which P(i) is growth limiting. Characterization of the PhoP protein has established that phosphorylation of the protein is not essential for PhoP dimerization or DNA binding but is essential for transcriptional regulation of Pho regulon genes. DNA footprinting studies of PhoP-regulated promoters showed that there was cooperative binding between PhoP dimers at PhoP-activated promoters and/or extensive PhoP oligomerization 3' of PhoP-binding consensus repeats in PhoP-repressed promoters. The crystal structure of PhoPN described in the accompanying paper revealed that the dimer interface between two PhoP monomers involves nonidentical surfaces such that each monomer in a dimer retains a second surface that is available for further oligomerization. A salt bridge between R113 on one monomer and D60 on another monomer was judged to be of major importance in the protein-protein interaction. We describe the consequences of mutation of the PhoP R113 codon to a glutamate or alanine codon and mutation of the PhoP D60 codon to a lysine codon. In vivo expression of either PhoP(R113E), PhoP(R113A), or PhoP(D60K) resulted in a Pho-negative phenotype. In vitro analysis showed that PhoP(R113E) was phosphorylated by PhoR (the cognate histidine kinase) but was unable to dimerize. Monomeric PhoP(R113E) approximately P was deficient in DNA binding, contributing to the PhoP(R113E) in vivo Pho-negative phenotype. While previous studies emphasized that phosphorylation was essential for PhoP function, data reported here indicate that phosphorylation is not sufficient as PhoP dimerization or oligomerization is also essential. Our data support the physiological relevance of the residues of the asymmetric dimer interface in PhoP dimerization and function.

Alkaline Phosphatase↗

Mutational analysis of Hsp90 alpha dimerization and subcellular localization: dimer disruption does not impede "in vivo' interaction with estrogen receptor.

The molecular chaperone Hsp90 has been found ubiquitously as a predominantly cytoplasmic dimer. By interacting with cytoplasmic or nuclear proteins such as pp60v-src or steroid receptors, Hsp90 helps its targets to become competent for full biological activity. Mutational deletion analysis of some properties of chicken Hsp90 alpha was undertaken after transient transfection of the constructs in COS7 cells. First, Hsp90 mutants were analyzed for their ability to behave as cytosolic dimers. We confirmed that the C-terminal Hsp90 region (amino acids 446-728) was sufficient for dimerization, and found that deletion of three small subregions in the 200 C-terminal residues precluded Hsp90 dimer formation. Moreover, we demonstrated that the N-terminal region of the protein (1-442) was not involved in dimerization. Second, the subcellular localization of the wild-type (WT) protein and mutants was analyzed by specific immunodetection and confocal microscopy. Most of the mutants were cytoplasmic like Hsp90WT, a nuclear localization being barely detectable in the WT protein or in mutants with a C-terminal truncation equal to or shorter than 286 residues. Surprisingly a mutant encoding the N-terminal region (1-285) was nuclear localized. In addition, the in vivo interaction between the cytoplasmic Hsp90 and the nuclear ER was documented after coexpression of both proteins in the same cells: some Hsp90 was shifted into the nucleus via its interaction with ER. From an analysis of dimeric or monomeric cytoplasmic Hsp90 mutants, we found that disruption of Hsp90 dimer did not systematically impede its interaction with ER. Finally, Hsp90WT and cytoplasmic mutants were tested for their ability to rescue from lethality a yeast strain deleted of both Hsp90 genes. Interestingly, the delta 661-677 mutant that showed an impaired dimerization but interacted with ER was able to confer viability, while the mutant deleted of the 30 C-terminal residues (NC6) was monomeric, did not confer viability and did not interact with ER. We therefore suggest that Hsp90 properties analyzed here are not necessarily interdependent.

Animals↗

The structure of MHC class II: a role for dimer of dimers.

The MHC class II molecules, expressed by antigen presenting cells, are heterodimers composed of an alpha and a beta chain, which function to present processed antigen to helper T cells. The human MHC class II molecules, HLA-DR1 and HLA-DR3, crystallized not as monomers, but rather dimers of alpha beta heterodimers. The 'dimer of dimers' or 'superdimer' structure led to speculation that the binding of T-cell receptors to monomeric class II molecules on the antigen presenting cell surface may affect dimerization and thus initiate signaling both in the T cell and in the antigen presenting cell. Recent biochemical analyses of the mouse MHC class II Ek molecule provide evidence that dimers of class II heterodimers form in the absence of T cells. Although such dimers were shown to augment T-cell stimulation, the dimerization of class II molecules alone is unlikely to initiate signal transduction. However, dimers may be important in stabilizing weak T-cell receptor/CD4/class II interactions, allowing further multimerization of such complexes, leading to signaling.

Animals↗

The dimerization of ferrihaems. IV. Studies on haematoferrihaem and a general appraisal of the nature and implications of dimerization.

The dimerization of haematoferrihaem was studied in phosphate buffer in the pH range 7.02--8.14. The absorbance of dilute solutions decreased over a period of several hours due to adsorption of haematoferrihaem to glass vessels. This problem was overcome by using dilute solutions within 10 min of preparation. Spectrophotometric data were consistent with a dimerization process according to the equation 2 monomer in equilibrium dimer + H+ as found earlier for other ferrihaems studied. The value of K, defined as K = [dimer] [H+]/[monomer]2, was found to be 1.00 . 10(-2). Rate constants for the forward and reverse steps in dimerization were determined at pH values of 6.63, 7.01 and 7.44, using the temperature-jump technique. The reaction pathway for dimerization was found to be similar to those of deuteroferrihaem and mesoferrihaem, but different from that of coproferrihaem. A general appraisal of the factors influencing dimerization is attempted in the light of accumulated data on various ferrihaems. With the exception of protoferrihaem, it is suggested that dimerzation increases with the hydrophobicity of the 2,4 substituents. The additional stability of the protoferrihaem dimer is explained in terms of increased interaction due to conjugation of the vinyl groups with the porphyrin macrocycle.

Adsorption↗

Performance evaluation of a new rapid quantitative assay system for measurement of D-dimer in plasma and whole blood: PATHFAST D-dimer.

D-dimer is an indicator for in vivo fibrin formation, reflecting the formation of fibrin crosslinked by factor XIIIa. D-dimer assays are frequently used in emergency situations, such as diagnosis of venous thrombosis and pulmonary embolism, or disseminated intravascular coagulation. In these conditions, short sample turnaround times are essential. The PATHFAST D-dimer assay allows rapid quantitative measurement of D-dimer in plasma and whole blood. The study shows an excellent correlation between whole blood and plasma measurement of D-dimer both in the high range, as well as in the normal range. Intra-assay and inter-assay coefficients of variation (CV) were below 10%. The upper limit of normal (ULN = mean value measured in 100 samples from healthy blood donors + 2 x S.D.) was approximately 1 microg/ml FEU, using the assay-specific calibration. The maximal value measured in 20 replicates of calibrator 1 containing no D-dimer antigen was 0.00052 microg/ml FEU, and this 10-fold lower than the declared detection limit of 0.005 microg/ml FEU. In conclusion, the PATHFAST D-dimer assay is the first automated fully quantitative D-dimer assay, which can use plasma and whole blood as sample materials in parallel.

Blood↗

HIV-1 genome dimerization: formation kinetics and thermal stability of dimeric HIV-1Lai RNAs are not improved by the 1-232 and 296-790 regions flanking the kissing-loop domain.

The genome of all retroviruses consists of two identical RNAs noncovalently linked near their 5' end. Dimerization of genomic RNA is thought to modulate several steps in the retroviral life cycle, such as recombination, translation, and encapsidation. The kissing-loop model of HIV-1 genome dimerization posits that the 233-285 region of the HIV-1 genome, by forming a hairpin and initiating dimerization through a loop-loop interaction, is at least the core dimerization domain of HIV-1 RNA. This region is called the kissing-loop domain. In addition, it can be argued that sequences within the 296-401 region [Paillart et al. (1994) J. Biol. Chem. 269, 27486-27493] or 5' of the primer binding site [Laughrea & Jetté (1996) Biochemistry 35, 1589-1598] might play some role in the dimerization process. Accordingly, we have studied the effect of regions 1-232 and 296-790 on the dimerization kinetics and thermal stability of HIV-1Lai RNAs containing the kissing-loop domain (HIV-1Lai is a typical representative of North American and European HIV-1 viruses). Experiments conducted at high and low ionic strength indicate that these regions have no strongly positive effect on the dimerization process. Our experiments also indicate that the kissing-loop domain of HIV-1Lai has an apparent dissociation temperature 13 degrees C higher than that of the HIV-1Mal kissing-loop domain (HIV-1Mal is a Central African virus whose kissing-loop domain has a "weak" GUGCAC autocomplementary sequence). Because the 296-401 region of HIV-1Mal RNA stabilizes dimeric RNAs by < or = 12 degrees C (Paillart et al., 1994), we infer that the contributions of sequences downstream of U295 are (at best) concealed in HIV-1Lai and in most American and European HIV-1 viruses, i.e., in viruses whose kissing-loop domain is characterized by a "strong" GCGCGC autocomplementary sequence.

Base Sequence↗

The dimer-dimer interaction surface of the replication terminator protein of Bacillus subtilis and termination of DNA replication.

The replication terminator protein (RTP) of Bacillus subtilis causes polar fork arrest at replication termini by sequence-specific interaction of two dimeric proteins with the terminus sequence. The crystal structure of the RTP protein has been solved, and the structure has already provide valuable clues regarding the structural basis of its function. However, it provides little information as to the surface of the protein involved in dimer-dimer interaction. Using site-directed mutagenesis, we have identified three sites on the protein that appear to mediate the dimer-dimer interaction. Crystallographic analysis of one of the mutant proteins (Y88F) showed that its structure is unaltered when compared to the wild-type protein. The locations of the three sites suggested a model for the dimer-dimer interaction that involves an association between two beta-ribbon motifs. This model is supported by a fourth mutation that was predicted to disrupt the interaction and was shown to do so. Biochemical analyses of these mutants provide compelling evidence that cooperative protein-protein interaction between two dimers of RTP is essential to impose polar blocks to the elongation of both DNA and RNA chains.

Bacillus subtilis↗

Extensive evaluation of the instrumentation laboratory IL test D-Dimer immunoturbidimetric assay on the ACL 9000 determines the D-Dimer cutoff value for reliable exclusion of venous thromboembolism.

The clinical diagnosis of venous thromboembolism (VTE), which includes both deep vein thrombosis (DVT) and pulmonary embolism (PE), is often difficult and requires a number of imaging tests plus clinical assessment. It is now accepted that pretest clinical probability of disease plus a sensitive, quantitative D-Dimer assay can be used to reliably exclude VTE. In design of diagnostic strategies for VTE it is recommended that the D-Dimer assay be evaluated for sensitivity and specificity in well-designed, blinded studies using a cohort of patients for whom the assay will ultimately be used. Therefore we evaluated the IL Test D-Dimer on the ACL 9000 automated coagulation analyzer for its sensitivity and specificity in the diagnosis of VTE. A total of 512 patients admitted to the emergency department of Providence Hospital with suspected VTE were included in the dataset. Our aim was to find the clinically meaningful IL Test D-Dimer cutoff value, which would give us 100% sensitivity and the highest possible specificity for exclusion of VTE. Patients were categorized clinically into low, medium, or high pretest probability and had computed tomographic and/or ventilation-perfusion scans for investigation of PE and ultrasound studies for suspected DVT, with the laboratory blinded to the clinical findings. Of the 511 patients, 28 (5.4%) had confirmed VTE (PE and/or DVT) based on imaging and clinical studies. Applying receiver operating characteristic curve (ROC) analysis, we determined from our study that a cutoff value of 237 ng/mL IL Test D-Dimer gave a 100% sensitivity with a specificity of 38% for detection of VTE. The findings demonstrate that a diagnostic strategy using the IL Test D-Dimer assay as a first-line test in combination with pretest probability is safe and can be used in patients with suspected VTE. In conclusion, patient analysis results indicating low or moderate pretest probability for VTE and a negative IL Test D-Dimer (cutoff value of 237 ng/mL) assay result on the ACL 9000 reliably exclude VTE (both PE and DVT). We expect that inclusion of the rapid IL Test D-Dimer assay for assessment of suspected VTE in the emergency department at Providence will result in improved patient diagnosis and therapy, reduction in unnecessary radiological investigations, and lowering of overall costs associated with investigation of patients suspected of having VTE disease.

Clinical Laboratory Techniques↗

Solution structure of the DNA decamer duplex containing a 3'-T x T basepair of the cis-syn cyclobutane pyrimidine dimer: implication for the mutagenic property of the cis-syn dimer.

The cis - syn dimer is the major DNA photoproduct produced by UV irradiation. In order to determine the origin of the mutagenic property of the cis - syn dimer, we used NMR restraints and molecular dynamics to determine the solution structure of a DNA decamer duplex containing a wobble pair between the 3'-T of the cis - syn dimer and the opposite T residue (CS/TA duplex). The solution structure of the CS/TA duplex revealed that the 3'-T x T base pair of the cis - syn dimer had base pair geometry that was significantly different from the canonical Watson-Crick base pair and caused destabilization and conformational distortion of its 3'-region. However, a 3'-T x A base pair at the cis - syn dimer within this related DNA decamer maintains the normal Watson-Crick base pair geometry and causes little distortion in the conformation of its 3'-side. Our results show that in spite of its stable hydrogen bonding, the insertion of a T residue opposite the 3'-T of the cis - syn dimer is inhibited by structural distortion caused by the 3'-T x T base pair. This may explain why the frequency of the 3'-T-->A transversion, which is the major mutation produced by the cis - syn dimer, is only 4%.

Base Pairing↗

Effects of peptide dimerization on pore formation: Antiparallel disulfide-dimerized magainin 2 analogue.

To elucidate the effects of peptide dimerization on pore formation by magainin 2 (MG2), a covalently linked antiparallel dimer of the MG2 analogue [(F5Y, L6C, F16W, I20C-MG2)(2): II] was synthesized based on the dimer structure revealed by our NMR study. The interactions of the dimer with lipid bilayers were investigated by CD and fluorescence in comparison with a monomer analogue (F5Y, F16W-MG2: I). Similar to I, II was found to form a peptide-lipid supramolecular complex pore accompanied with lipid flip-flop and peptide translocation. The pore formed by II was characterized by a slightly larger pore diameter and a threefold longer lifetime than that of I, although the pore formation rate of the dimer was lower than that of the monomer. The coexistence of the dimer and the monomer exhibited slight but significant synergism in membrane permeabilization, which was maximal at a monomer/dimer ratio of 3. Therefore, we concluded that a pentameric pore composed of one pore-stabilizing dimer and three monomers maximized the overall leakage activity in keeping with our kinetic prediction.

Amino Acid Sequence↗

Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface.

The stability of tetrameric malate dehydrogenase from the green phototrophic bacterium Chloroflexus aurantiacus (CaMDH) is at least in part determined by electrostatic interactions at the dimer-dimer interface. Since previous studies had indicated that the thermal stability of CaMDH becomes lower with increasing pH, attempts were made to increase the stability by removal of (excess) negative charge at the dimer-dimer interface. Mutation of Glu165 to Gln or Lys yielded a dramatic increase in thermal stability at pH 7.5 (+23.6 -- + 23.9 degrees C increase in apparent t(m)) and a more moderate increase at pH 4.4 (+4.6 -- + 5.4 degrees C). The drastically increased stability at neutral pH was achieved without forfeiture of catalytic performance at low temperatures. The crystal structures of the two mutants showed only minor structural changes close to the mutated residues, and indicated that the observed stability effects are solely due to subtle changes in the complex network of electrostatic interactions in the dimer-dimer interface. Both mutations reduced the concentration dependency of thermal stability, suggesting that the oligomeric structure had been reinforced. Interestingly, the two mutations had similar effects on stability, despite the charge difference between the introduced side-chains. Together with the loss of concentration dependency, this may indicate that both E165Q and E165K stabilize CaMDH to such an extent that disruption of the inter-dimer electrostatic network around residue 165 no longer limits kinetic thermal stability.

Bacterial Proteins↗

Tandem dimerization of the human p53 tetramerization domain stabilizes a primary dimer intermediate and dramatically enhances its oligomeric stability.

Tetramerization of the human p53 tumor suppressor protein is required for its biological functions. However, cellular levels of p53 indicate that it exists predominantly in a monomeric state. Since the oligomerization of p53 involves the rate-limiting formation of a primary dimer intermediate, we engineered a covalently linked pair of human p53 tetramerization (p53tet) domains to generate a tandem dimer (p53tetTD) that minimizes the energetic requirements for forming the primary dimer. We demonstrate that p53tetTD self-assembles into an oligomeric structure equivalent to the wild-type p53tet tetramer and exhibits dramatically enhanced oligomeric stability. Specifically, the p53tetTD dimer exhibits an unfolding/dissociation equilibrium constant of 26 fM at 37 degrees C, or a million-fold increase in stability relative to the wild-type p53tet tetramer, and resists subunit exchange with monomeric p53tet. In addition, whereas the wild-type p53tet tetramer undergoes coupled (i.e. two-state) dissociation/unfolding to unfolded monomers, the p53tetTD dimer denatures via an intermediate that is detectable by differential scanning calorimetry but not CD spectroscopy, consistent with a folded p53tetTD monomer that is equivalent to the p53tet primary dimer. Given its oligomeric stability and resistance against hetero-oligomerization, dimerization of p53 constructs incorporating the tetramerization domain may yield functional constructs that may resist exchange with wild-type or mutant forms of p53.

Calorimetry, Differential Scanning↗

Synthesis and screening of a random dimeric peptide library using the one-bead-one-dimer combinatorial approach.

Large combinatorial libraries of random peptides have been used for a variety of applications that include analysis of protein-protein interactions, epitope mapping, and drug targeting. The major obstacle in screening these libraries is the loss of specific but low affinity binding peptides during washing steps. Loss of these specific binders often results in isolation of peptides that bind nonspecifically to components used in the selection process. Previously, it has been demonstrated that dimerizing or multimerizing a peptide can remarkably improve its binding kinetics by 10- to 1000-fold due to an avidity effect. To take advantage of this observation, we constructed a random library of 12 amino acid dimeric peptides on polyethylene glycol acrylamide (PEGA) beads by modifying the 'one-bead-one-compound' approach. The chemical synthesis of 100,000 peptides as dimers can be problematic due to steric and aggregation effects and the presence of many peptide sequences that are difficult to synthesize. We have designed a method, described in detail here, to minimize the problems inherent in the synthesis of a dimeric library by modifying the existing 'split and pool' synthetic method. Using this approach the dimeric library was used to isolate a series of peptides that bound selectively to epithelial cancer cells. One peptide with the amino acid sequence QMARIPKRLARH bound as a dimer to prostate cancer cells spiked into the blood but did not bind to circulating hematopoeitic cells. The monomeric form of this peptide, however, did not bind well to the same LNCaP cell line. These data demonstrate that "hits" obtained from such a 'one-bead-one-dimer' library can be used directly for the final application or used as leads for construction of second generation libraries.

Amino Acid Sequence↗

Epitope-dependent blocking of the angiotensin-converting enzyme dimerization by monoclonal antibodies to the N-terminal domain of ACE: possible link of ACE dimerization and shedding from the cell surface.

In a biomembrane modeling system, reverse micelles, somatic ACE forms dimers via carbohydrate-mediated interaction, providing evidence for the existence of a carbohydrate-recognizing domain on the ACE molecule. We localized this putative region on the N-domain of ACE using monoclonal antibodies (mAbs) to seven different epitopes of ACE. Two mAbs, 9B9 and 3G8, directed to distinct, but overlapping, epitopes of the N-domain of ACE shielded the CRD. Only "simple" ACE-antibody complexes were found in the system. Five mAbs allowed the formation of "double" antibody-ACE-ACE-antibody complexes via carbohydrate-mediated interactions. The results were confirmed using the ACE N- and C-domains. Testicular ACE was unable to form carbohydrate-mediated ACE dimers in the reverse micelles, while the N-domain of ACE, obtained by limited proteolysis of the parent full-length ACE, retained the ability to form dimers. Furthermore, mAb 3G8, which blocked ACE dimerization in micelles, significantly inhibited ACE shedding from the surface of ACE-expressing cells. Galactose prevented ACE dimerization in reverse micelles and also affected antibody-induced ACE shedding in an epitope-dependent manner. Restricted glycosylation of somatic ACE, obtained by the treatment of CHO-ACE cells with the glucosidase inhibitor N-butyldeoxynojirimycin, significantly increased the rate of basal ACE shedding and altered antibody-induced ACE shedding. A chemical cross-linking approach was used to show that ACE is present (at least in part) as noncovalently linked dimers on the surface of CHO-ACE cells. These results suggest a possible link between putative ACE dimerization on the cell surface and the proteolytic cleavage (shedding) of ACE.

1-Deoxynojirimycin↗

Mechanism of folding of the dimeric core domain of Escherichia coli trp repressor: a nearly diffusion-limited reaction leads to the formation of an on-pathway dimeric intermediate.

A polypeptide corresponding to the core/dimerization domain of E. coli Trp repressor (TR), [2-66]2 TR, was constructed by insertion of a pair of stop codons into the trpR gene. The kinetic properties of the urea-induced folding of this core fragment were examined by intrinsic tryptophan fluorescence (FL) and circular dichroism (CD) spectroscopy. The kinetic response of wild-type TR (WT TR) is very complicated and has been interpreted to involve three parallel channels with multiple folding and isomerization reactions (Mann et al. (1995) Biochemistry 34, 14573-14580). The refolding of [2-66]2 TR can be described by a much simpler mechanism, involving an association reaction followed by a urea-dependent first-order folding reaction. The second-order rate constant for the association reaction approaches that of the diffusion limit, 3 x 10(8) M-1 s-1 in 1 M urea at 15 degreesC. Double-jump experiments demonstrate that >/=93% of the unfolded monomers proceed to the native dimer via the dimeric intermediate; several lines of evidence demonstrate that this dimeric species is an on-pathway intermediate. The subsequent first-order folding reaction of the dimeric intermediate to the native species involves development of additional secondary structure and tertiary structure. The kinetic folding mechanism of [2-66]2 TR suggests that: (1) the complexity of the folding kinetics of full-length WT TR arises from alternative interactions of the DNA reading heads with the dimerization core domain-not from the intertwined nature of the dimerization interface; (2) residues 2-66 contain all of the sequence information necessary to direct the near-diffusion-limited association reaction in a TR folding reaction; and (3) the formation of secondary and tertiary structure is concurrent with or precedes dimerization, and further development certainly follows the formation of quaternary structure.

Bacterial Proteins↗

Molecular recognition thermodynamics of bile salts by beta-cyclodextrin dimers: Factors governing the cooperative binding of cyclodextrin dimers.

The complex stability constants (K(S)), standard molar enthalpy (DeltaH degrees), and entropy changes (DeltaS degrees) for the inclusion complexation of two families of beta-cyclodextrin (beta-CD) dimers, i.e. beta-CD dimers Se1-Se4 bearing 2,2'-diselenobis(benzoyl) tether (Se-dimers) and beta-CD dimers Py1-Py4 bearing 2,2'-bipyridine-4,4'-dicarboxy tether (Py-dimers), with four bile salt guests, i.e. sodium cholate (CA), sodium deoxycholate (DCA), sodium glycocholate (GCA), and sodium taurocholate (TCA), were determined at 25 degrees C in Tris buffer solution (pH 7.4) at 298.15 K by means of isothermal titration microcalorimetry. The thermodynamic parameters obtained, together with the ROESY spectra of interactions between beta-CD dimers and bile salts, consistently suggest that the length, flexibility, and structure of spacers linking the two beta-CD cavities not only determine the binding modes but also significantly alter the molecular selectivity of beta-CD dimers.

Calorimetry↗