Showing papers on "Cooperativity published in 2003"
TL;DR: The shape of the funnel bottom, which depicts the stability of the native state ensemble, also accounts for the thermodynamic parameters of activation that characterize these extremophilic enzymes, therefore providing a rational basis for stability-activity relationships in protein adaptation to extreme temperatures.
441 citations
TL;DR: The present method underscores the fact that positive cooperativity in artificial self-assembling systems is probably much more rare than it was previously thought.
Abstract: A method has been proposed to assess cooperativity in self-assembly processes. The method is based on a clear distinction between intermolecular and intramolecular processes which are compared with the corresponding reference reactions. It has been applied to two classical cases, namely the self-assembly of helicates and of porphyrin ladders, by using data previously published by the groups of Lehn and Anderson, respectively. Contrarily to the conclusions of the authors, pointing out self-assembly processes driven by positive cooperativity, the method here presented indicates in both cases the absence of cooperative effects. The methods previously used to assess cooperativity, in particular Scatchard plot and/or Hill plot, are criticized as being inappropriate for self-assembly, because they are pertinent to a specific case only, namely the intermolecular binding of a monovalent ligand L to a multivalent receptor M, a case very different from self-assembly which involves both inter- and intramolecular int...
274 citations
TL;DR: The full implications of the free energy were tested by including another type of peptide, melittin, that forms toroidal pores, instead of barrel-stave pores as in the case of alamethicin, indicating that the membrane thinning effect is a plausible mechanism for the peptide-induced pore formations.
270 citations
TL;DR: In this paper, the authors measured potentiometric titration curves of weak polyelectrolytes, PAH1 and PAA, interpolyelectron complexes PAH/PAA, PDADMAC−PAA and PAH−PSS, and multilayered microcapsules.
Abstract: We have measured potentiometric titration curves of the weak polyelectrolytes, PAH1 and PAA, interpolyelectrolyte complexes PAH−PAA, PDADMAC−PAA, and PAH−PAA, prepared by mixing of the polyelectrolyte solutions, and multilayered microcapsules made by layer-by-layer adsorption of the same pairs of oppositely charged polyelectrolytes onto CaCO3 microspheres(PAH/PAA)5, (PDADMAC/PAA)5, and (PAH/PSS)5. The data were analyzed within the frame of an Ising model taking into account the nearest-neighbor interaction between proton binding sites. The anticooperative character of proton binding with PAH (cooperativity parameter q = 0.13) was shown to become a highly cooperative process in the interpolyelectrolyte complex PAH−PSS and multilayered microcapsules (PAH/PSS)5, q ≈ 2−3. The cooperativity of the process is increased also for complexes PDADMAC−PAA and PAH−PAA and for multilayered shells (PDADMAC/PAA)5 and (PAH/PAA)5; however, the cooperativity parameter q remains below unity for the PDADMAC−PAA system or a li...
216 citations
TL;DR: It is proposed that MRP2 contains two similar but nonidentical ligand binding sites: one site from which substrate is transported and a second site that regulates the affinity of the transport site for the substrate.
196 citations
TL;DR: CD spectroscopic studies of Cu2+ binding to various fragments of the octarepeat region of the prion protein show that glycine and l-histidine will successfully compete for all Cu2- ions bound to the PrP octapeptide region, suggestingCu2+ coordinates with a lower affinity for PrP than the fm dissociation constant reported previously.
195 citations
TL;DR: This is the first demonstration that there is an intrinsic tendency of Hb to undergo T-->R2 transition, induced by purely elastic forces of entropic origin that are uniquely defined for the particular contact topology of the T form.
191 citations
TL;DR: In this article, a mixed DFT/AM1 procedure was used for the entire helical structures, while AM1 was initially used to optimize the side chains, followed by reoptimization at the DFT level.
Abstract: Five peptides, each containing 17 amino acids, have been completely geometrically optimized in their α-helical and β-strand forms using a mixed DFT/AM1 procedure. B3LYP/D95** was used for the entire helical structures, while AM1 was initially used to optimize the side chains, followed by reoptimization at the DFT level. The energetic and structural results show (1) that the helices are favored over the strands by 29.5 to 37.4 kcal/mol; (2) that alkyl groups on the amino acid side chains favor helix formation even in the absence of solvent; (3) that C−H···O hydrogen bonds contribute to the relative stability of the helices that contain amino acids (val, leu and ile) with β-hydrogens in their alkyl side chains; (4) that formation of these helices entails approximately 6.6 kcal/mol of strain within the backbone per hydrogen bond; and (5) that H-bond cooperativity is essential for the α-helix to become more stable than a corresponding β-strand. This last observation strongly suggests that pairwise potentials ...
185 citations
TL;DR: It is shown that arbitrarily chosen foreign DNA binding proteins, LexA and Tet repressor, cooperate with an adjacently binding endogenous activator protein, Gcn4, to coactivate expression of chromosomal reporter genes in Saccharomyces cerevisiae, implying that collaborative competition contributes to gene regulation in vivo.
Abstract: The mechanism by which gene regulatory proteins gain access to their DNA target sites is not known. In vitro, binding is inherently cooperative between arbitrary DNA binding proteins whose target sites are located within the same nucleosome. We refer to such competition-based cooperativity as collaborative competition. Here we show that arbitrarily chosen foreign DNA binding proteins, LexA and Tet repressor, cooperate with an adjacently binding endogenous activator protein, Gcn4, to coactivate expression of chromosomal reporter genes in Saccharomyces cerevisiae. Coactivation requires that the cooperating target sites be within a nucleosome-length distance; it leads to increased occupancy by Gcn4 at its binding site; and it requires both Gcn5 and Swi/Snf which, at an endogenous Gcn4-dependent promoter, act subsequent to Gcn4 binding. These results imply that collaborative competition contributes to gene regulation in vivo. They further imply that, even in the presence of the cell's full wild-type complement of chromatin remodeling factors, competition of regulatory proteins with histone octamer for access to regulatory target sites remains a quantitative determinant of gene expression levels. We speculate that initial target site recognition and binding may occur via spontaneous nucleosomal site exposure, with remodeling factor action required downstream to lock in higher levels of regulatory protein occupancy.
180 citations
TL;DR: Eleven bis-ureas have been synthesized, and some of their properties are reported, including the fact that the formation of dimers is less favored than that of long oligomers.
Abstract: Eleven bis-ureas have been synthesized, and some of their properties are reported. Several of these compounds form supramolecular polymers in organic solvents. The self-association is shown by FTIR spectroscopy to display cooperativity at two levels. The first level of cooperativity is due to the synergistic association of the two urea functions of a single molecule. The second level of cooperativity is revealed by the fact that the formation of dimers is less favored than that of long oligomers.
178 citations
TL;DR: A processive-clamp model is proposed for the catalytic cycle of Mdl1p in which association and dissociation of the NBDs depends on the status of bound nucleotides.
TL;DR: Analysis of a hierarchy of continuum Langevin dynamics models of chymotrypsin inhibitor 2 suggests that interaction mechanisms more intricate than simple Gō-like constructs and pairwise additive solvation-like contributions are needed to rationalize some of the most basic generic protein properties.
TL;DR: This work has examined the extensible unfolding of red cell spectrins as monomeric constructs of just two, three, or four repeats from the actin-binding ends of both alpha- and beta-chains, i.e., alpha(18-21) and beta(1-4) or their subfragments.
TL;DR: The individual H-bond energies at the B3LYP/D95 level for linear chains of H bonding formamides containing from 2 to 15 monomeric units were calculated in this article.
Abstract: The individual H-bond energies have been calculated at the B3LYP/D95** level for linear chains of H-bonding formamides containing from 2 to 15 monomeric units. The cooperative effect upon the stron...
TL;DR: Using electron microscopy, five different states of RecA-DNA filaments are reconstructed and a model generated shows that the nucleotide binding core is substantially rotated from its position in the RecA crystal filament, resulting in ATP binding between subunits.
TL;DR: The x-ray structure of CSPMbraA6, a 112-aa antennal protein from the moth Mamestra brassicae (Mbra), was shown to exhibit a novel type of α-helical fold and binding cooperativity was demonstrated for some ligands, suggesting a stepwise binding.
Abstract: Chemosensory proteins (CSPs) have been proposed to transport hydrophobic chemicals from air to olfactory or taste receptors. They have been isolated from several sensory organs of a wide range of insect species. The x-ray structure of CSPMbraA6, a 112-aa antennal protein from the moth Mamestra brassicae (Mbra), was shown to exhibit a novel type of α-helical fold. We have performed a structural and binding study of CSPMbraA6 to get some insights into its possible molecular function. Tryptophan fluorescence quenching demonstrates the ability of CSPMbraA6 to bind several types of semio-chemicals or surrogate ligands with μM Kd. Its crystal structure in complex with one of these compounds, 12-bromo-dodecanol, reveals extensive conformational changes on binding, resulting in the formation of a large cavity filled by three ligand molecules. Furthermore, binding cooperativity was demonstrated for some ligands, suggesting a stepwise binding. The peculiar rearrangement of CSPMbraA6 conformation and the cooperativity phenomenon might trigger the recognition of chemicals by receptors and induce subsequent signal transduction.
TL;DR: In this paper, a systematic study of V gene families carried out with consensus VH and VL domains alone and in combinations in the scFv format was carried out, and they found comparatively low expression yields and lower cooperativity in equilibrium unfolding in antibody fragments containing VH domains of human germline families.
Abstract: In a systematic study of V gene families carried out with consensus VH and VL domains alone and in combinations in the scFv format, we found comparatively low expression yields and lower cooperativity in equilibrium unfolding in antibody fragments containing VH domains of human germline families 2, 4, and 6. From an analysis of the packing of the hydrophobic core, the completeness of charge clusters, the occurrence of unsatisfied hydrogen bonds, and residues with low ‚-sheet propensities, positive … angles, and exposed hydrophobic side chains, we pinpointed residues potentially responsible for the unsatisfactory properties of these germline-encoded sequences. Several of those are in common between the domains of the even-numbered subgroups, but do not occur in the odd-numbered ones. In this study, we have systematically exchanged those residues alone and in combination in two different scFvs using the VH6 framework, and we describe their effect on equilibrium stability and folding yield. We improved the stability by 20.9 kJ/mol and the expression yield by a factor of 4 and can now use these data to rationally engineer antibodies derived from this and similar germline families for better biophysical properties. Furthermore, we provide an improved design for libraries exploiting the significant additional diversity provided by these frameworks. Both antibodies studied here completely retain their binding affinity, demonstrating that the CDR conformations were not affected. 1 Abbreviations: CDR, complementary determining region; GdnHCl, guanidine hydrochloride; HuCAL, Human Combinatorial Antibody Library; IMAC, immobilized metal ion affinity chromatography; IPTG, isopropyl ‚-D-thiogalactopyranoside; scFv, single-chain antibody frag- ment consisting of the variable domains of the heavy and light chains connected by a peptide linker; VH, variable domain of the heavy chain of an antibody; VL, variable domain of the light chain of an antibody. 1517
TL;DR: It is shown that copper cooperatively stimulates catalytic activity of WNDP and that this effect requires the presence of both MBS5 and MBS6 and the MBS1–5 mutants have a 7–8-fold lower EC50 for copper activation, suggesting that their affinity for copper is increased.
TL;DR: A polypeptide, BspCBM17/CBM28, comprising the tandem CBMs from Cel5A, bound to amorphous cellulose with a significantly higher affinity than the sum of the affinities ofCcCBM 17 and Bsp cbm28, indicating cooperativity between the linked CBMs.
TL;DR: It is characteristic of eukaryotic transcription that a unique combination of multiple transcriptional regulatory proteins bound to promoter DNA specifically activate or repress downstream target genes; this is referred to as combinatorial gene regulation.
TL;DR: In this article, the energy of polyalanine chains in the α-helical and extended structure was studied by employing density-functional theory, where the full peptide−peptide connectivity (backbone) of proteins was considered.
Abstract: We studied the energetics of finite and infinite polyalanine chains in the α-helical and extended structure by employing density-functional theory. On the basis of these results we extracted the energy of hydrogen bonds (hb's) and their interactions by taking the full peptide−peptide connectivity (backbone) of proteins into account. We focus on two limiting cases: an isolated hb and one within an infinite α-helical chain. In the infinite chain the cooperativity within an infinite network of hb's strengthens each individual bond by more than a factor of 2. This effect has important consequences for the stability of α-helices.
TL;DR: This study confirms the central role of weak interactions in regulating the balance between stability and activity of an enzyme in order to adapt to the environmental temperature.
TL;DR: Five pentapeptides, GGGGG, GAGGG, GVGGG, GL GGG, and GIGGG, have been completely optimized in the 3(10)-helical and open beta-strand conformations at the B3LYP/D95 level.
Abstract: Five pentapeptides, GGGGG, GAGGG, GVGGG, GLGGG, and GIGGG, have been completely optimized in the 3(10)-helical and open beta-strand conformations at the B3LYP/D95 level. The energies of the helices relative to the beta-strands vary from -2.1 to -3.6 kcal and depend on the amino acid residue sequence. The energies of substituting A, V, L, or I for G in the second position are also presented. Vibrational analyses were performed on the optimized structures. Vibrational coupling through the individual H-bond chains of the helices is confirmed to be stronger than that through space or through the covalent bonds. The cooperative interactions of the H-bonds are evident from both the structures and the coupling of the amide I, amide II, and N-H vibrations.
TL;DR: A general kinetic model is developed, which predicts an unexpected multiplicative increase in affinity as a function of ligand sites and suggests that a previously undescribed mechanism may underlie certain cooperative interactions.
TL;DR: It is shown that large cosolvent-induced changes in the CD spectrum, in contrast with the modest effects observed on Halpha chemical shifts, support a hydrophobically collapsed entropy-driven conformation in water whose stability is modulated by long-range Coulombic interactions from the Glu-Lys interactions.
Abstract: A model β-hairpin peptide has been used to investigate the context-dependent contribution of cross-strand Lys−Glu interactions to hairpin stability. We have mutated two Ser−Lys interstrand pairs to Glu−Lys salt bridges, one close to the type I‘ Asn−Gly turn sequence (Ser6 → Glu), and one close to the N- and C-termini (Ser15 → Glu). Each individual interaction contributes ∼1.2−1.3 kJ mol-1 to stability; however, introducing the two salt bridges simultaneously produces a much larger overall contribution (−3.6 kJ mol-1) consistent with an important role for preorganization and cooperativity in determining the energetics of weak interactions. We compare and contrast CD and NMR data on the highly folded hairpin with the two Glu−Lys pairs to shed light on the nature of the folded state in water. We show that large cosolvent-induced changes in the CD spectrum, in contrast with the modest effects observed on Hα chemical shifts, support a hydrophobically collapsed entropy-driven conformation in water whose stabili...
TL;DR: It is shown that in the binding of biotin to streptavidin, the streptavin structure becomes better packed, and it is concluded that this contraction of the strePTavidin structure promotes biotin binding.
TL;DR: A minimalist quasi‐equilibrium model is proposed to explore qualitatively the STR taking into account cooperative recognition of the promoter/enhancer and synergy and it is shown that a sigmoidal response to a morphogenetic gradient can be used to generate a nested gradient of another morphogen.
Abstract: A sigmoidal transcriptional response (STR) is thought to act as a molecular switch to control gene expression. This nonlinear behaviour arises as a result of the cooperative recognition of a promoter/enhancer by transcription factors (TFs) and/or their synergy to attract the basal transcriptional machinery (BTM). Although this cooperation between TFs is additive in terms of energy, it leads to an exponential increase in affinity between the BTM and the pre-initiation complexes. This exponential increase in the strength of interactions is the principle that governs synergistic systems. Here, I propose a minimalist quasi-equilibrium model to explore qualitatively the STR taking into account cooperative recognition of the promoter/enhancer and synergy. Although the focus is on the effect of activators, a similar treatment can be applied to inhibitors. One of the main insights obtained from the model is that generation of a sigmoidal threshold is possible even in the absence of cooperative DNA binding provided the TFs synergistically interact with the BTM. On the contrary, when there is cooperative binding, the impact of synergy diminishes. It will also be shown that a sigmoidal response to a morphogenetic gradient can be used to generate a nested gradient of another morphogen. Previously, I had proposed that halving the amounts of TFs involved in sigmoidal transcriptional switches could account for the abnormal dominant phenotypes associated with some of these genes. This phenomenon, called haploinsufficiency (HI), has been recognised as the basis of many human diseases. Although a formal proof linking HI and a sigmoidal response is lacking, it is tempting to explore the model from the perspective of dosage effects.
TL;DR: The results support previous arguments that the cooperative folding of simple, single-domain proteins gives rise to their topology-dependent folding rates and speculate that this cooperativity may have arisen in order to generate the smooth energetic landscapes upon which rapid folding can occur.
TL;DR: Interactions of Atox1 with wild-type and mutated pairs of the MBSs of MNK are investigated using yeast two-hybrid analysis and real-time surface plasmon resonance (SPR) to demonstrate the power and sensitivity of SPR as compared with other, more indirect methods.
TL;DR: This study has revealed important features of molecular mechanisms in the biochemical network describing PKG-Iβ activation by cGMP, yielding new insight into ligand activation of cyclic nucleotide-dependent protein kinases, a class of regulatory proteins that is key to many cellular processes.
Abstract: Using small-angle x-ray scattering, we have observed the cGMP-induced elongation of an active, cGMP-dependent, monomeric deletion mutant of cGMP-dependent protein kinase (Δ1–52PKG-Iβ). On saturation with cGMP, the radius of gyration of Δ1–52PKG-Iβ increases from 29.4 ± 0.1 Å to 40.1 ± 0.7 Å, and the maximum linear dimension increases from 90 Å ± 10% to 130 Å ± 10%. The elongation is due to a change in the interaction between structured regulatory (R) and catalytic (C) domains. A model of cGMP binding to Δ1–52PKG-Iβ indicates that elongation of Δ1–52PKG-Iβ requires binding of cGMP to the low-affinity binding site of the R domain. A comparison with cAMP-dependent protein kinase suggests that both elongation and activation require cGMP binding to both sites; cGMP binding to the low-affinity site therefore seems to be a necessary, but not sufficient, condition for both elongation and activation of Δ1–52PKG-Iβ. We also predict that there is little or no cooperativity in cGMP binding to the two sites of Δ1–52PKG-Iβ under the conditions used here. Results obtained by using the Δ1–52PKG-Iβ monomer indicate that a previously observed elongation of PKG-Iα is consistent with a pure change in the interaction between the R domain and the C domain, without alteration of the dimerization interaction. This study has revealed important features of molecular mechanisms in the biochemical network describing PKG-Iβ activation by cGMP, yielding new insight into ligand activation of cyclic nucleotide-dependent protein kinases, a class of regulatory proteins that is key to many cellular processes.