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Neira J.L.,University Miguel Hernández | Neira J.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos | Camara-Artigas A.,University of Almeria
Archives of Biochemistry and Biophysics | Year: 2017

The alpha splice variant of p73 (p73α), a homologue of the tumour suppressor p53, has at its C terminus a sterile alpha motif (SAM); this domain, SAMp73, is involved in lipid binding and it is thought to mediate in protein-protein interactions. As SAMp73 is a 68-residue-long helical bundle, it could be a good model to study the (2,2,2-trifluoroethanol) TFE-induced conformational transitions of α-helical proteins. Furthermore, as SAMp73 binds to lipids through a well-known polypeptide patch, we can test whether TFE is a good mimic of lipids and membranes. To address those questions, we used several biophysical probes, namely, fluorescence, circular dichroism, 1D, 2D and 3D-NMR spectroscopies, and dynamic light scattering. The TFE-induced conformational transition of SAMp73 was complex, involving several species as detected by the biophysical probes. The last TFE-induced transition occurred at a concentration of TFE of ∼20% (v/v), where the protein lost its compactness. None of those TFE-induced species accumulated during the two-state folding of SAMp73 in aqueous solution. The final state at 40% TFE was highly helical, but its structure was not rigid. For SAMp73, TFE did not properly mimic a membrane-like environment, since at very low TFE concentrations, other residues, together with those known to interact with lipids, were also affected by the co-solvent. Comparison with studies on isolated peptides, comprising the helical regions of SAMp73, suggests that peptides were good models of the intact protein in TFE. © 2017


Domenech R.,University Miguel Hernández | Bocanegra R.,Autonomous University of Madrid | Gonzalez-Muniz R.,Institute Quimica Medica IQM CSIC | Gomez J.,University Miguel Hernández | And 3 more authors.
Biomacromolecules | Year: 2011

The C-terminal domain (CTD) of the capsid protein (CA) of HIV-1 participates both in the formation of CA hexamers and in the joining of hexamers through homodimerization to form the viral capsid. Intact CA and the CTD are able to homodimerize with similar affinity (∼15 μM); CTD homodimerization involves mainly an α-helical region. We have designed peptides derived from that helix with predicted higher helical propensities than the wild-type sequence while keeping residues important for dimerization. These peptides showed a higher helicity than that of the wild-type peptide, although not as high as theoretically predicted, and proved to be able to self-associate with apparent affinities similar to that of the whole CTD. However, binding to CTD mainly occurs at the last helical region of the protein. Accordingly, most of those peptides are unable to inhibit CA polymerization in vitro. Therefore, there is a subtle tuning between monomer-monomer interactions important for CTD dimerization and the maximal helical content achieved by the wild-type sequence of the interface. © 2011 American Chemical Society.


Neira J.L.,University Miguel Hernández | Neira J.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos | Sevilla P.,Complutense University of Madrid | Sevilla P.,CSIC - Institute for the Structure of Matter | Garcia-Blanco F.,Complutense University of Madrid
Physical Chemistry Chemical Physics | Year: 2012

The α-splice variant of p73 (p73α), a homologue of the tumour suppressor p53, has close to its C terminus a sterile alpha motif (SAM), SAMp73, that is involved in protein-biomolecule interactions. The conformational stability of SAMp73 is low (∼5 kcal mol-1), although its thermal stability is high. To explain this high thermostability, we studied the dynamics of SAMp73 over a wide range of GdmCl (guanidine hydrochloride) concentrations and temperatures by NMR relaxation, NMR hydrogen-exchange (HX) and fluorescence lifetime approaches. The slowest exchanging residues of SAMp73 belong to the helical regions, and they did exchange by a global unfolding process. Moreover, SAMp73 was very flexible, with most of its amide protons affected by slow μs-ms conformational exchange. Within this time scale, the residues of SAMp73 with the largest exchange rates (Rex) were involved in binding with other molecules; therefore, the flexibility in the μs-ms range was associated with biological functions. As the [GdmCl] increased, the pico-to-nanosecond flexibility of the backbone amide protons raised, but it did so differently depending on the residue. We were able to obtain, for the first time, the linear [GdmCl]-variation of the local conformational entropies, mSi, which ranged from 5.3 to 0.3 cal mol-1 K-1 M-1, similar to those measured by using macroscopic techniques in other proteins. Conversely, the temperature dependence of the pico-to-nanosecond dynamics of the backbone amide protons of SAMp73 indicates that the flexibility of some residues decreased with the temperature; these results explain the high thermostability of the protein. © 2012 The Owner Societies.


Domenech R.,University Miguel Hernández | Bocanegra R.,Autonomous University of Madrid | Velazquez-Campoy A.,Institute Biocomputacion Y Fisica Of Sistemas Complejos | Neira J.L.,University Miguel Hernández | Neira J.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos
Biochimica et Biophysica Acta - Proteins and Proteomics | Year: 2011

Assembly of the mature human immunodeficiency virus type 1 (HIV-1) capsid involves the oligomerization of the capsid protein, CA. During retroviral maturation, the CA protein undergoes structural changes and forms exclusive intermolecular interfaces in the mature capsid shell, different from those in the immature precursor. The most conserved region of CA, the major homology region (MHR), is located in the C-terminal domain of CA (CTD). The MHR is involved in both immature and mature virus assembly; however, its exact function during both assembly stages is unknown. To test its conformational preferences and to provide clues on its role during CA assembly, we have used a minimalist approach by designing a peptide comprising the whole MHR (MHRpep, residues Asp152 to Ala174). Isolated MHRpep is mainly unfolded in aqueous solution, with residual structure at its C terminus. MHRpep binds to monomeric CTD with an affinity of ~ 30 μM (as shown by fluorescence and ITC); the CTD binding region comprises residues belonging to α-helices 10 and 11. In the immature virus capsid, the MHR and α-helix 11 regions of two CTD dimers also interact [Briggs JAG, Riches JD, Glass B, Baratonova V, Zanetti G and Kräusslich H-G (2009) Proc. Natl. Acad. Sci. USA 106, 11090-11095]. These results can be considered a proof-of-concept that the conformational preferences and binding features of isolated peptides derived from virus proteins could be used to mimic early stages of virus assembly. © 2011 Elsevier B.V. All rights reserved.


Benavides-Riveros C.L.,University of Zaragoza | Benavides-Riveros C.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos | Toranzo I.V.,University of Granada | Dehesa J.S.,University of Granada
Journal of Physics B: Atomic, Molecular and Optical Physics | Year: 2014

The ground-state entanglement of a single particle of the N-harmonium system (i.e., a completely integrable model of N particles where both the confinement and the two-particle interaction are harmonic) is shown to be analytically determined in terms of N and the relative interaction strength. For bosons, we compute the von Neumann entropy of the one-body reduced density matrix by using the corresponding natural occupation numbers. A critical number, Nc, of particles exists, and below it, for positive values of the coupling constant, the entanglement grows when the number of particles increases; the opposite occurs for . For fermions, we compute the one-body reduced density matrix for the closed-shell spinned case. In the strong coupling regime, the linear entropy of the system decreases when N grows. For fixed N, the entanglement is found (a) to decrease (increase) for negatively (positively) increases values of the coupling constant, and (b) to grow when the energy increases. Moreover, the spatial and spin contributions to the total entanglement are found to be of comparable size. © 2014 IOP Publishing Ltd.


Benavides-Riveros C.L.,University of Zaragoza | Benavides-Riveros C.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos | Benavides-Riveros C.L.,Saarland University | Springborg M.,Saarland University | Springborg M.,Tianjin University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2015

Postulated by Pauli to explain the electronic structure of atoms and molecules, the exclusion principle establishes an upper bound of 1 for fermionic natural occupation numbers {ni}. A recent analysis of the pure N-representability problem provides a wide set of inequalities for the {ni}, leading to constraints on these numbers. This has a strong potential impact on reduced density matrix functional theory as we know it. In this work we continue our study of the nature of these inequalities for some atomic and molecular systems. The results indicate that (quasi)saturation of some of them leads to selection rules for the dominant configurations in configuration interaction expansions, in favorable cases providing means for significantly reducing their computational requirements. © 2015 American Physical Society. ©2015 American Physical Society.


Domenech R.,University Miguel Hernández | Neira J.L.,University Miguel Hernández | Neira J.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos
Current Protein and Peptide Science | Year: 2013

HIV-1, the agent responsible for AIDS, belongs to the retrovirus family. Assembly of the immature HIV-1 capsid occurs through the controlled polymerization of the Gag polyprotein, which is transported to the plasma membrane of infected cells, where morphogenesis of the immature, non-infectious virion occurs. Moreover, the mature capsid of HIV-1 is formed by the assembly of copies of the capsid protein (CA), which results, among other proteins, from cleavage of Gag. The C-terminal domain of CA (CTD) can homodimerize, and most of the dimerization interface is formed by a single α-helix from each monomer. Assembly of the HIV-1 capsid critically depends on CA-CA interactions, including CTD interaction with itself and with the N-terminal domain of CA (NTD). This review will report on recent advances for the search of small organic compounds and peptides that have been designed in the last four years to hamper CA assembly. Most of the molecules have been proved to interact with CA; such molecules aim to disrupt and/or alter the oligomerization capability of CTD and/or NTD. © 2013 Bentham Science Publishers.


Neira J.L.,University Miguel Hernández | Neira J.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos
Archives of Biochemistry and Biophysics | Year: 2013

NMR spectroscopy is one of the few biophysical methods that can provide atomic-level insight into the conformation of partially folded states and/or intermediates present along the protein folding pathway. Such studies are important not only within the context of the protein folding problem, but also to push forward the technique, due to the challenging nature of the systems studied. In fact, new NMR methods have been created, and applied, in an attempt to characterize the conformational features of the states along the folding pathway. Describing the structures along the folding landscape is of key importance to comprehend the folding reaction, design new proteins and to understand how several polypeptide chains are implicated in pathogenic amyloid states. The last advances in several approaches, which use NMR: (i) to monitor the protein folding pathway and/or, (ii) to characterize the structure of the intermediate states in such reaction are reviewed in this work. © 2012 Elsevier Inc. All rights reserved.


Neira J.L.,University Miguel Hernández | Neira J.L.,Institute Biocomputacion Y Fisica Of Sistemas Complejos
Archives of Biochemistry and Biophysics | Year: 2014

The alpha splice variant of p73 (p73α), a homologue of the tumour suppressor p53, has at its C terminus a sterile alpha motif (SAM); this domain, SAMp73, is involved in lipid binding and it is thought to mediate in protein-protein interactions. SAMp73 is composed of five helices (α1-α5). In this work, we dissected SAMp73 in fragments encompassing the different helices, to study the conformational stability of the isolated elements of secondary structure. There was no evidence of stable residual helical structure in the isolated α1, α4 and α5 helices in aqueous solution, as shown by 2D-1H NMR and far-UV CD spectroscopies; those helices acquired native-like helical structure in the presence of 40% trifluoroethanol (TFE). The population of helical structure in α5 seemed to be driven by the indole moiety of Trp542, and it was enhanced by the presence of α4. On the other hand, helices α2 and 310(α3) had a tendency to self-associate even in TFE-water solutions. However, the short, aggregation-prone 310(α3) helix was key to attain the native-like fold of SAMp73, as suggested by experiments with non-covalent complexes among the peptides. © 2014 Elsevier Inc. All rights reserved.


Petretti S.,Humboldt University of Berlin | Vanne Y.V.,Humboldt University of Berlin | Saenz A.,Humboldt University of Berlin | Castro A.,Institute Biocomputacion Y Fisica Of Sistemas Complejos | Decleva P.,University of Trieste
Physical Review Letters | Year: 2010

The ionization probability of N2, O2, and CO2 in intense laser fields is studied theoretically as a function of the alignment angle by solving the time-dependent Schrödinger equation numerically assuming only the single-active-electron approximation. The results are compared to recent experimental data and good agreement is found for N2 and O2. For CO2 a possible explanation is provided for the failure of simplified single-active-electron models to reproduce the experimentally observed narrow ionization distribution. It is based on a field-induced coherent core-trapping effect. © 2010 The American Physical Society.

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