186,606 research outputs found
Local structural disorder imparts plasticity on linear motifs
No full textMotivation: The dynamic nature of protein interaction networks requires fast and transient molecular switches. The underlying recognition motifs (linear motifs, LMs) are usually short and evolutionarily variable segments, which in several cases, such as phosphorylation sites or SH3-binding regions, fall into locally disordered regions. We probed the generality of this phenomenon by predicting the intrinsic disorder of all LM-containing proteins enlisted in the Eukaryotic Linear Motif (ELM) database. Results: We demonstrated that LMs in average are embedded in locally unstructured regions, while their amino acid composition and charge/ hydropathy properties exhibit a mixture characteristic of folded and disordered proteins. Overall, LMs are constructed by grafting a few specificity-determining residues favoring structural order on a highly flexible carrier region. These results establish a connection between LMs and molecular recognition elements of intrinsically unstructured proteins (IUPs), which realize a non-conventional mode of partner binding mostly in regulatory functions. © The Author 2007. Published by Oxford University Press. All rights reserved
Fuzzy Complexes: Polymorphism And Structural Disorder In Protein-protein Interactions
No full textThe notion that all protein functions are determined through macromolecular interactions is the driving force behind current efforts that aim to solve the structures of all cellular complexes. Recent findings, however, demonstrate a significant amount of structural disorder or polymorphism in protein complexes, a phenomenon that has been largely overlooked thus far. It is our view that such disorder can be classified into four mechanistic categories, covering a continuous spectrum of structural states from static to dynamic disorder and from segmental to full disorder. To emphasize its generality and importance, we suggest a generic term, 'fuzziness', for this phenomenon. Given the crucial role of protein disorder in protein-protein interactions and in regulatory processes, we envision that fuzziness will become integral to understanding the interactome. © 2007 Elsevier Ltd. All rights reserved
Presence of Tompa Shine-Dalgarno as function of antiSD.
No full textPresence of Tompa Shine-Dalgarno as function of antiSD.</p
Preformed structural elements feature in partner recognition by intrinsically unstructured proteins
No full textIntrinsically unstructured proteins (IUPs) are devoid of extensive structural order but often display signs of local and limited residual structure. To explain their effective functioning, we reasoned that such residual structure can be crucial in their interactions with their structured partner(s) in a way that preformed structural elements presage their final conformational state. To check this assumption, a database of 24 IUPs with known 3D structures in the bound state has been assembled and the distribution of secondary structure elements and backbone torsion angles have been analysed. The high proportion of residues in coil conformation and with φ, ψ angles in the disallowed regions of the Ramachandran map compared to the reference set of globular proteins shows that IUPs are not fully ordered even in their bound form. To probe the effect of partner proteins on IUP folding, inherent conformational preferences of IUP sequences have been assessed by secondary structure predictions using the GOR, ALB and PROF algorithms. The accuracy of predicting secondary structure elements of IUPs is similar to that of their partner proteins and is significantly higher than the corresponding values for random sequences. We propose that strong conformational preferences mark regions in IUPs (mostly helices), which correspond to their final structural state, while regions with weak conformational preferences represent flexible linkers between them. In our interpretation, preformed elements could serve as initial contact points, the binding of which facilitates the reeling of the flexible regions onto the template. This finding implies that IUPs draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner. © 2004 Elsevier Ltd. All rights reserved
DETERMINATION OF CONTROL PARAMETERS FOR RC1 REACTION SYSTEM
No full textV diplomskem delu opisujemo določanje vrednosti regulacijskih parametrov reakcijskega kalorimetra RC1e Mettler Toledo in reaktorskega sistema EasyMax 102 Mettler Toledo. Parametre smo določali z metodo po Ziegler-ju in Nichols-u. Ta metoda temelji na regulacijskem sistemu brez povratne zanke. Vrednosti za povratno zanko smo izračunali z Excelovim diagramom, s katerim smo izračunali P in I regulacijska parametra. Reaktor RC1e smo uporabili za poskuse z večjimi volumni, medtem ko EasyMax za tiste z manjšmi. Oba reakcijska sistema sta avtomatizirana, kar pomeni, da računalnik sam regulira podane veličine. Poskuse smo izvajali pri različnih temperaturah, vrtilnih hitrostih mešala, volumnih in različnih gostotah medija. Dobljene vrednosti regulacijskih parametrov smo prikazali grafično v odvisnosti fizikalnih sprememb v sistemu. Ugotovili smo, da je P parameter odvisen od vseh prej omenjenih fizikalnih sprememb, medtem ko I parameter ni odvisen od vrtilne hitrosti mešala v reakcijski zmesi. Z reakcijo nevtralizacije smo preverili vpliv vrednosti regulacijskih parametrov na temperaturni odziv ter določili entalpije nevtralizacije. Dokazali smo, da so bili regulacijski parametri pravilno določeni, saj je bil odziv sistema brez osciliranja temperature v reaktorju, hkrati se je temperatura hitro vzpostavila na željeno vrednost.This dissertation is concerned with determining values of regulatory parameters for the reactor calorimeter RC1e Mettler Toledo and reactor system EasyMax 102 Mettler Toledo. Values of parameters were obtained using Ziegler and Nichols methods. The later relies on regulatory configuration without feedback loop. Values for the feedback loop were therefore calculated using Excel diagram, from which P and I regulatory parameters were obtained. RC1e reactor was used for large-volume experiments, while EasyMax was utilised for experiments in smaller volumes. Both systems were automated, meaning all provided values were computer regulated. Experiments were carried out at different temperatures, mixing velocities and volumes, as well as with mediums of varying densities. Experimental values of regulatory parameters were consequently plotted against physical changes in the system, providing us with the final results. We discovered that P parameter depends on all previously listed physical factors, whilst I parameter does not depend upon mixing velocity of the reaction mixture. By performing neutralising reaction, we determined the effect of regulatory parameter values over the temperature response and by doing so, we defined neutralisation enthalpy. With this we confirmed that previously determined regulatory parameters were correct, as the system quickly established the set temperature and the temperature did not oscillate during the operation
Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP
No full textPhosphorylation at Ser-133 of the kinase inducible domain of CREB (KID) triggers its binding to the KIX domain of CBP via a concomitant coil-to-helix transition. The exact role of this key event is still puzzling: it does not switch between disordered and ordered states, nor its direct interactions fully account for selectivity. Hence, we reasoned that phosphorylation may shift the conformational preferences of KID towards a binding-competent state. To this end we investigated the intrinsic structural properties of the unbound KID in phosphorylated and unphosphorylated forms by simulated annealing and molecular dynamics simulations. Although helical populations show subtle differences, phosphorylation reduces the flexibility of the turn segment connecting the two helices in the complexed structure and induces a transient structural element that corresponds to its bound conformation. It is stabilized by the pSer-133-Arg-131 interaction, which is absent from the unphosphorylated KID. Diminishing this coupling decreases the 3.1 kcal/mol contribution of pSer-133 to the binding free energy (ΔGbind) of the phosphorylated KID to KIX by 1.1 kcal/mol, as computed in reference to Ser-133. In a binding competent form of the S133E KID mutant, the contribution of Glu-133 to ΔG bind is by 1.5 kcal/mol smaller than that of pSer, suggesting that altered structural properties due to pSer → Glu replacement impair the binding affinity. Thus, we propose that phoshorylation contributes to selectivity not merely by the direct interactions of the phosphate group with KIX, but also by promoting the formation of a transient structural element in the highly conserved turn segment. © 2006 Wiley-Liss, Inc
Intrinsic disorder in cell signaling and gene transcription
No full textStructural disorder, which enables unique modes of action often associated with molecular recognition and folding induced by a partner, is widespread in eukaryotic proteomes. Due to the ensuing advantages, such as specificity without strong binding, adaptability to multiple partners and subtle regulation by post-translational modification, structural disorder is prevalent in proteins of signaling and regulatory functions, such as membrane receptors, scaffold proteins, cytoskeletal proteins, transcription factors and nuclear hormone receptors. In this review we survey the most important aspects of structural disorder, with major focus on features and advantages pertinent to signal transduction. Our major goal is to elucidate how the functional requirements of these protein classes concur with specific functional modes disorder enables.open
Distinct Hydration Properties of Wild-Type and Familial Point Mutant A53T of α-Synuclein Associated with Parkinson's Disease
No full textAbstractThe propensity of α-synuclein to form amyloid plays an important role in Parkinson's disease. Three familial mutations, A30P, E46K, and A53T, correlate with Parkinson's disease. Therefore, unraveling the structural effects of these mutations has basic implications in understanding the molecular basis of the disease. Here, we address this issue through comparing details of the hydration of wild-type α-synuclein and its A53T mutant by a combination of wide-line NMR, differential scanning calorimetry, and molecular dynamics simulations. All three approaches suggest a hydrate shell compatible with a largely disordered state of both proteins. Its fine details, however, are different, with the mutant displaying a somewhat higher level of hydration, suggesting a bias to more open structures, favorable for protein-protein interactions leading to amyloid formation. These differences disappear in the amyloid state, suggesting basically the same surface topology, irrespective of the initial monomeric state
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