Biomedical subjects

Roberto Sanchez

Publications and source records attributed to Roberto Sanchez.

9 recordsLinked to original sources

PubMed2006

Variable gap penalty for protein sequence-structure alignment.

The penalty for inserting gaps into an alignment between two protein sequences is a major determinant of the alignment accuracy. Here, we present an algorithm for finding a globally optimal alignment by dynamic programming that can use a variable gap penalty (VGP) function of any form. We also describe a specific function that depends on the structural context of an insertion or deletion. It penalizes gaps that are introduced within regions of regular secondary structure, buried regions, straight segments and also between two spatially distant residues. The parameters of the penalty function were optimized on a set of 240 sequence pairs of known structure, spanning the sequence identity range of 20-40%. We then tested the algorithm on another set of 238 sequence pairs of known structures. The use of the VGP function increases the number of correctly aligned residues from 81.0 to 84.5% in comparison with the optimized affine gap penalty function; this difference is statistically significant according to Student's t-test. We estimate that the new algorithm allows us to produce comparative models with an additional approximately 7 million accurately modeled residues in the approximately 1.1 million proteins that are detectably related to a known structure.

Algorithms↗

PubMed2005

Accuracy of structure-derived properties in simple comparative models of protein structures.

The accuracy of comparative models of proteins is addressed here. A set of 12,732 single-template models of sequences of known high-resolution structures was built by an automated procedure. Accuracy of several structure-derived properties, such as surface area, residue accessibility, presence of pockets, electrostatic potential and others, was determined as a function of template:target sequence identity by comparing models with their corresponding experimental structures. As expected, the average accuracy of structure-derived properties always increases with higher template:target sequence identity, but the exact shape of this relationship can differ from one property to another. A comparison of structure-derived properties measured from NMR and X-ray structures of the same protein shows that for most properties, the NMR/X-ray difference is of the same order as the error in models based on approximately 40% template:target sequence identity. The exact sequence identity at which properties reach that accuracy varies between 25 and 50%, depending on the property being analyzed. A general characteristic of simple comparative models is that their surface has increased area as a consequence of being more rugged than that of experimental structures. This suggests that including solvent effects during model building or refinement could significantly improve the accuracy of surface properties in comparative models.

Amino Acids↗

PubMed2004

Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation.

Lysine acetylation of the tumor suppressor protein p53 in response to a wide variety of cellular stress signals is required for its activation as a transcription factor that regulates cell cycle arrest, senescence, or apoptosis. Here, we report that the conserved bromo-domain of the transcriptional coactivator CBP (CREB binding protein) binds specifically to p53 at the C-terminal acetylated lysine 382. This bromodomain/acetyl-lysine binding is responsible for p53 acetylation-dependent coactivator recruitment after DNA damage, a step essential for p53-induced transcriptional activation of the cyclin-dependent kinase inhibitor p21 in G1 cell cycle arrest. We further present the three-dimensional nuclear magnetic resonance structure of the CBP bromodomain in complex with a lysine 382-acetylated p53 peptide. Using structural and biochemical analyses, we define the molecular determinants for the specificity of this molecular recognition.

Amino Acid Sequence↗

PubMed2004

Systematic analysis of added-value in simple comparative models of protein structure.

Added-value is the additional information that a model carries with respect to the template structure used for model building. Thousands of single-template models, corresponding to proteins of known structure, were analyzed. The accuracy of structure-derived properties, such as residue accessibility, surface area, electrostatic potential, and others, was determined as a function of template:target sequence identity by comparing the models with their corresponding experimental structures. Added-value was determined by comparing the accuracy in models with that from templates. Geometry-dependent properties such as neighborhood of buried residues and accessible surface area showed low added-value. Properties that also depend on the protein sequence, such as presence of polar areas and electrostatic potential, showed high added-value. In general added-value increases when template:target sequence identity decreases, but it is also affected by alignment errors. This study justifies the use of models instead of the use of templates to estimate structure-derived properties of a target protein.

Algorithms↗

PubMed2004

Bacillus subtilis YhcR, a high-molecular-weight, nonspecific endonuclease with a unique domain structure.

In a continuing effort to identify ribonucleases that may be involved in mRNA decay in Bacillus subtilis, fractionation of a protein extract from a triple-mutant strain that was missing three previously characterized 3'-to-5' exoribonucleases (polynucleotide phosphorylase [PNPase], RNase R, and YhaM) was undertaken. These experiments revealed the presence of a high-molecular-weight nuclease encoded by the yhcR gene that was active in the presence of Ca(2+) and Mn(2+). YhcR is a sugar-nonspecific nuclease that cleaves endonucleolytically to yield nucleotide 3'-monophosphate products, similar to the well-characterized micrococcal nuclease of Staphylococcus aureus. YhcR appears to be located principally in the cell wall and is likely to be a substrate for a B. subtilis sortase. Zymogram analysis suggests that YhcR is the major Ca(2+)-activated nuclease of B. subtilis. In addition to having a unique overall domain structure, YhcR contains a hitherto unknown structural domain that we have named "NYD," for "new YhcR domain."

Amino Acid Sequence↗

PubMed2004

Vitamin C is a kinase inhibitor: dehydroascorbic acid inhibits IkappaBalpha kinase beta.

Reactive oxygen species (ROS) are key intermediates in cellular signal transduction pathways whose function may be counterbalanced by antioxidants. Acting as an antioxidant, ascorbic acid (AA) donates two electrons and becomes oxidized to dehydroascorbic acid (DHA). We discovered that DHA directly inhibits IkappaBalpha kinase beta (IKKbeta) and IKKalpha enzymatic activity in vitro, whereas AA did not have this effect. When cells were loaded with AA and induced to generate DHA by oxidative stress in cells expressing a constitutive active IKKbeta, NF-kappaB activation was inhibited. Our results identify a dual molecular action of vitamin C in signal transduction and provide a direct linkage between the redox state of vitamin C and NF-kappaB signaling events. AA quenches ROS intermediates involved in the activation of NF-kappaB and is oxidized to DHA, which directly inhibits IKKbeta and IKKalpha enzymatic activity. These findings define a function for vitamin C in signal transduction other than as an antioxidant and mechanistically illuminate how vitamin C down-modulates NF-kappaB signaling.

Adenosine Triphosphate↗

PubMed2002

Structure, upstream promoter region, and functional domains of a mouse and human Mix paired-like homeobox gene.

Mix/Bix proteins represent a vertebrate subgroup of paired-like homeodomain proteins which are known to function around the time of gastrulation. Here we report the structures of the genomic and upstream promoter regions of a mouse and human Mix-like gene. Both genes map to syntenic regions of chromosome 1 and contain two coding exons, with the paired-type homeodomain split between the exons within helix 3. Differentiating mouse embryonic stem cells transcribe a messenger RNA of approximately 2.6 kb. The first exon encodes the translation initiation codon and a 5' untranslated region of approximately 90 bp. Sequence analysis of the 960 bp upstream of the transcription start site of the mouse Mix gene revealed the presence of a putative initiator region and TATA box as well as potential Smad, FoxH1/FAST, T-box, COUP-TF, C/EBP, GATA, HNF3 binding sites and retinoic acid response elements. A number of these sites are conserved in the human Mix promoter. We find that most paired-related homeodomain proteins, including mouse and human Mix, contain a proline-rich region within their amino termini which may interact with other proteins. Mouse and human Mix proteins contain highly conserved carboxy-terminal polar/acidic regions with the potential to form an amphipathic helix and the ability to activate transcription in yeast. Mouse Mix expressed in COS cells or in vitro binds a DNA consensus sequence identified previously for paired class homeodomain proteins. These studies suggest that a number of features of paired-like protein structure and function are conserved across diverse species and provide a useful framework for studying the function and regulation of the mouse Mix gene.

Amino Acid Sequence↗

PubMed2002

The (beta)gamma subunits of G proteins gate a K(+) channel by pivoted bending of a transmembrane segment.

The molecular mechanism of ion channel gating remains unclear. Using approaches such as proline scanning mutagenesis and homology modeling, we localize the gate of the K(+) channels controlled by the (beta)gamma subunits of G proteins at the pore-lining bundle crossing of the second transmembrane (TM2) helices. We show that the flexibility afforded by a highly conserved glycine residue in the middle of TM2 is crucial for channel gating. In contrast, flexibility introduced immediately below the gate disrupts gating. We propose that the force produced by channel-G(beta)gamma interactions is transduced through the rigid region below the helix bundle crossing to bend TM2 at the glycine that serves as a hinge and open the gate.

Amino Acid Sequence↗

PubMed2002

Bacillus subtilis YhaM, a member of a new family of 3'-to-5' exonucleases in gram-positive bacteria.

A strain of Bacillus subtilis lacking two 3'-to-5' exoribonucleases, polynucleotide phosphorylase (PNPase) and RNase R, was used to purify another 3'-to-5' exoribonuclease, which is encoded by the yhaM gene. YhaM was active in the presence of Mn(2+) (or Co(2+)), was inactive in the presence of Mg(2+), and could also degrade single-stranded DNA. The half-life of bulk mRNA in a mutant lacking PNPase, RNase R, and YhaM was not significantly different from that of the wild type, suggesting the existence of additional activities that can participate in mRNA turnover. Sequence homologues of YhaM were found only in gram-positive organisms. The Staphylococcus aureus homologue, CBF1, which had been characterized as a double-stranded DNA binding protein involved in plasmid replication, was also shown to be an Mn(2+)-dependent exoribonuclease. YhaM protein has a C-terminal "HD domain," found in metal-dependent phosphohydrolases. By structure modeling, it was shown that YhaM also contains an N-terminal "OB-fold," present in many oligosaccharide- and oligonucleotide-binding proteins. The combination of these two domains is unique. Thus, YhaM and 10 related proteins from gram-positive organisms constitute a new exonuclease family.

Amino Acid Sequence↗