Biomedical subjects

Armando Albert

Publications and source records attributed to Armando Albert.

10 recordsLinked to original sources

PubMed2006

Cell signaling and function organized by PB1 domain interactions.

The PB1-domain-containing proteins p62, aPKC, MEKK2/MEKK3, MEK5, and Par-6 play roles in critical cell processes like osteoclastogenesis, angiogenesis, and early cardiovascular development or cell polarity. PB1 domains are scaffold modules that adopt the topology of ubiquitin-like beta-grasp folds that interact with each other in a front-to-back mode to arrange heterodimers or homo-oligomers. The different PB1 domain adaptors provide specificity for PB1 kinases to ensure the effective transmission of cellular signals. Also, recent data suggest that PB1 domains may serve to orchestrate signaling cascades not involving other PB1 domains, such as the MEK5-ERK5 and p62-ERK1 interactions.

Adaptor Proteins, Signal Transducing↗

PubMed2005

Structural basis for membrane anchorage of viral phi29 DNA during replication.

Prokaryotic DNA replication is compartmentalized at the cellular membrane. Functional and biochemical studies showed that the Bacillus subtilis phage 29-encoded membrane protein p16.7 is directly involved in the organization of membrane-associated viral DNA replication. The structure of the functional domain of p16.7 in complex with DNA, presented here, reveals the multimerization mode of the protein and provides insights in the organization of the phage genome at the membrane of the infected cell.

Bacillus subtilis↗

PubMed2005

Structure of the functional domain of phi29 replication organizer: insights into oligomerization and dna binding.

The Bacillus subtilis phage phi29-encoded membrane protein p16.7 is one of the few proteins involved in prokaryotic membrane-associated DNA replication that has been characterized at a functional and biochemical level. In this work we have determined both the solution and crystal structures of its dimeric functional domain, p16.7C. Although the secondary structure of p16.7C is remarkably similar to that of the DNA binding homeodomain, present in proteins belonging to a large family of eukaryotic transcription factors, the tertiary structures of p16.7C and homeodomains are fundamentally different. In fact, p16.7C defines a novel dimeric six-helical fold. We also show that p16.7C can form multimers in solution and that this feature is a key factor for efficient DNA binding. Moreover, a combination of NMR and x-ray approaches, combined with functional analyses of mutants, revealed that multimerization of p16.7C dimers is mediated by a large protein surface that is characterized by a striking self-complementarity. Finally, the structural analyses of the p16.7C dimer and oligomers provide important clues about how protein multimerization and DNA binding are coupled.

Binding Sites↗

PubMed2004

The structure of the Arabidopsis thaliana SOS3: molecular mechanism of sensing calcium for salt stress response.

The Arabidopsis thaliana SOS3 gene encodes a calcium sensor that is required for plant salt tolerance. The SOS3 protein binds to and activates the self-inhibited SOS2 protein kinase, which mediates the expression and activities of various transporters important for ion homeostasis under salt stress. SOS3 belongs to a unique family of calcium-binding proteins that contain two pairs of EF hand motifs with four putative metal-binding sites. We report the crystal structure of a dimeric SOS3 protein in complex with calcium, and with calcium and manganese. Analytical ultracentrifugation experiments and circular dichroism measurements show that calcium binding is responsible for the dimerization of SOS3. This leads to a change in the global shape and surface properties of the protein that may be sufficient to transmit the Ca(2+) signal elicited during salt stress.

Amino Acid Sequence↗

PubMed2004

Functional characterization of the yeast Ppz1 phosphatase inhibitory subunit Hal3: a mutagenesis study.

Saccharomyces cerevisiae Hal3 is a conserved protein that binds the carboxyl-terminal catalytic domain of the PP1c (protein phosphatase 1)-related phosphatase Ppz1 and potently inhibits its activity, thus modulating all of the characterized functions so far of the phosphatase. It is unknown how Hal3 binds to Ppz1 and inhibits its activity. Although it contains a putative protein phosphatase 1c binding-like sequence (263KLHVLF268), mutagenesis analysis suggests that this motif is not required for Ppz1 binding and inhibition. The mutation of the conserved His378 (possibly involved in dehydrogenase catalytic activity) did not impair Hal3 functions or Ppz1 binding. Random mutagenesis of the 228 residue-conserved central region of Hal3 followed by a loss-of-function screen allowed the identification of nine residues important for Ppz1-related Hal3 functions. Seven of these residues cluster in a relatively small region spanning from amino acid 446 to 480. Several mutations affected Ppz1 binding and inhibition in vitro, whereas changes in Glu460 and Val462 did not alter binding but resulted in Hal3 versions unable to inhibit the phosphatase. Therefore, there are independent Hal3 structural elements required for Ppz1 binding and inhibition. S. cerevisiae encodes a protein (Vhs3) structurally related to Hal3. Recent evidence suggests that both mutations are synthetically lethal. Surprisingly, versions of Hal3 carrying mutations that strongly affected Ppz1 binding or inhibitory capacity were able to complement lethality. In contrast, the mutation of His378 did not. This finding suggests that Hal3 may have both Ppz1-dependent and independent functions involving different structural elements.

Amino Acid Motifs↗

PubMed2004

Peptide AS-48: prototype of a new class of cyclic bacteriocins.

After the discovery of bacteriocin AS-48, a 70-residue cyclic peptide produced by Enterococcus faecalis subsp. liquefaciens, some naturally-occurring cyclic proteins from bacteria have been reported. AS-48 is encoded by the 68-kb pheromone-responsive plasmid pMB2, and the gene cluster involved in production and immunity has been identified and sequenced. This peptide exerts a bactericidal action on sensitive cells (most of the Gram-positive and some Gram-negative bacteria). Its target is the cytoplasmic membrane, in which it opens pores, leading to the dissipation of the proton motive force and cell death, a mechanism similar to that proposed for the action of defensins or, most generally, cationic antibacterial peptides. This fact, together with its remarkable stability and solubility over a wide pH range, suggest that this bacteriocin could be a good candidate as a natural food preservative. The amino acid composition of purified AS-48 shows the absence of modified or dehydrated residues, making it clearly different from lantibiotics. Bacteriocin AS-48 also differs from defensins in that it does not contain cysteines and consequently no disulfide bridges, which makes is high stability even more remarkable. Composition analysis of AS-48 shows a high proportion of basic to acidic amino acids, conferring to this peptide a strong basic character, with an isoelectric point close to 10.5. Determination of the AS-48 structural gene DNA sequence, together with the sequences of AS-48 protease digestion fragments and mass spectrometry determinations, allowed us to determine unambiguously the cyclic structure of the molecule, being the first example of a posttranslational modification in which a cyclic structure arises from a "head-to-tail" linkage. We have solved the three-dimensional structure of AS-48 in solution, and it consists of a globular arrangement of five alpha-helices enclosing a compact hydrophobic core. Interestingly, the head-to-tail peptide link between Trp-70 and Met-1 lies in the middle of alpha-helix 5, which is shown to have a pronounced effect on the stability of the three-dimensional structure. Analysis of structure-function relationship allowed us to propose models to understand the aspects of the molecular function of AS-48. The purpose of this work is to review recent developments in our understanding about the biochemical and biological characteristics and structure of this unusual type of bacteriocin.

Animals↗

PubMed2003

Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1.

Pneumococcal bacteriophage-encoded lysins are modular choline binding proteins that have been shown to act as enzymatic antimicrobial agents (enzybiotics) against streptococcal infections. Here we present the crystal structures of the free and choline bound states of the Cpl-1 lysin, encoded by the pneumococcal phage Cp-1. While the catalytic module displays an irregular (beta/alpha)(5)beta(3) barrel, the cell wall-anchoring module is formed by six similar choline binding repeats (ChBrs), arranged into two different structural regions: a left-handed superhelical domain configuring two choline binding sites, and a beta sheet domain that contributes in bringing together the whole structure. Crystallographic and site-directed mutagenesis studies allow us to propose a general catalytic mechanism for the whole glycoside hydrolase family 25. Our work provides the first complete structure of a member of the large family of choline binding proteins and reveals that ChBrs are versatile elements able to tune the evolution and specificity of the pneumococcal surface proteins.

Bacteriophages↗

PubMed2002

Crystallization and preliminary X-ray diffraction studies of the complete modular endolysin from Cp-1, a phage infecting Streptococcus pneumoniae.

Endolysin from the phage Cp-1 (Cpl-1) cleaves the glycosidic beta1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the pneumococcal cell wall. Cpl-1 has been crystallized using the hanging-drop vapour-diffusion method at 291 K. Diffraction-quality orthorhombic crystals of the native protein were obtained only after addition of the detergent n-decyl-beta-D-maltoside. Crystals belong to space group C222(1), with unit-cell parameters a = 77.949, b = 95.782, c = 129.282 A. Diffraction data to a resolution of 2.1 A were collected at a synchrotron facility.

Crystallization↗

PubMed2002

TrwD, the hexameric traffic ATPase encoded by plasmid R388, induces membrane destabilization and hemifusion of lipid vesicles.

TrwD, a hexameric ATP hydrolase encoded by plasmid R388, is a member of the PulE/VirB11 protein superfamily of traffic ATPases. It is essential for plasmid conjugation, particularly for expression of the conjugative W pilus. In the present study, we analyzed the effects that TrwD produced on unilamellar vesicles consisting of cardiolipin and phosphatidylcholine in equimolar amounts. TrwD induced dose-dependent vesicle aggregation and intervesicular mixing of the lipids located in the outer monolayers in the presence of calcium. It also induced extensive leakage of the vesicular aqueous contents. A point mutant of TrwD with a mutation in the P loop of the nucleotide-binding region (K203Q) that lacks both ATPase activity and the ability to support conjugation showed the same behavior as native TrwD in all of these processes, which were independent of the presence of ATP. Structure prediction methods revealed a close similarity to Helicobacter pylori protein HP0525, another member of the PulE/VirB11 family, whose crystal structure is known. The interpretation of our data in the light of this structure is that TrwD interacts with the lipid bilayer through hydrophobic regions in its N-terminal domain, which leads to a certain degree of membrane destabilization. TrwD appears to be a part of the conjugation machinery that interacts with the membranous systems in order to facilitate DNA transfer in bacteria.

Adenosine Triphosphatases↗

PubMed1996

Synthesis, Characterization, and Theoretical Study of Sulfur-Containing Donor-Acceptor DCNQI Derivatives with Photoinduced Intramolecular Electron Transfer.

The donor-acceptor compounds N,N'-dicyanobenzo[b]naphtho[2,3-e][1,4]dithiin-6,11-quinonediimine (9a) and N,N'-dicyanobenzo[b]naphtho[2,3-e][1,4]oxathiin-6,11-quinonediimine (10a) and their methyl-substituted derivatives (9b and 10b-d, respectively) have been prepared, and their structural and electronic properties have been characterized by both experimental techniques and quantum-chemical calculations. The (1)H-NMR spectra evidence the existence of a syn/anti isomerism in solution. Both experimental and theoretical data suggest that the preferred configuration of the N-CN groups corresponds to a syn isomer for 9 and to an anti isomer for 10. The X-ray analysis performed for 9b reveals that molecules are not planar and pack in vertical stacks showing an overlap between donor and acceptor moieties of adjacent molecules. In agreement with X-ray data, theoretical calculations predict that both for 9 and 10 the acceptor DCNQI moiety is folded and adopts a butterfly-type structure and the donor moiety is bent along the line passing through the heteroatoms. The energy difference between planar and butterfly structures is calculated to be < 3 kcal/mol at the ab initio 6-31G level. The UV-vis spectra present a broad absorption in the visible which corresponds to a photoinduced intramolecular electron transfer from the high-energy HOMO furnished by the donor moiety to the low-energy LUMO located on the DCNQI fragment. Cyclic voltammetry displays one oxidation peak to the cation and two one-electron reduction waves to the anion and dianion. Theoretical calculations show the planarization of the acceptor/donor moiety induced by reduction/oxidation. The formation of stable radical anions is corroborated by the intense EPR signals recorded for reduced 9. The assignment of the hyperfine coupling constants of the EPR spectra is consistent with the existence of a preferred syn configuration.

Journal Article↗