Biomedical subjects

Luis Serrano

Publications and source records attributed to Luis Serrano.

At least 19 recordsLinked to original sources

PubMed2025

Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map.

Essentiality studies have traditionally focused on coding regions, often overlooking other small genetic regulatory elements. To address this, we combined transposon libraries containing promoter or terminator sequences to obtain a high-resolution essentiality map of a genome-reduced bacterium, at near-single-nucleotide precision when considering non-essential genes. By integrating temporal transposon-sequencing data by k-means unsupervised clustering, we present a novel essentiality assessment approach, providing dynamic and quantitative information on the fitness contribution of different genomic regions. We compared the insertion tolerance and persistence of the two engineered libraries, assessing the local impact of transcription and termination on cell fitness. Essentiality assessment at the local base-level revealed essential protein domains and small genomic regions that are either essential or inaccessible to transposon insertion. We also identified structural regions within essential genes that tolerate transposon disruptions, resulting in functionally split proteins. Overall, this study presents a nuanced view of gene essentiality, shifting from static and binary models to a more accurate perspective. Additionally, it provides valuable insights for genome engineering and enhances our understanding of the biology of genome-reduced cells.

DNA Transposable Elements↗

PubMed2025

Exon inclusion signatures enable accurate estimation of splicing factor activity.

Splicing factors control exon inclusion in messenger RNAs, shaping transcriptome and proteome diversity. Their catalytic activity is regulated by multiple layers, making single-omic measurements on their own fall short in identifying which splicing factors underlie a phenotype. Here, we posit that splicing factor activity can be estimated from changes in exon inclusion. To test this hypothesis, we benchmarked methods for constructing splicing factor→exon networks and estimating splicing factor activity. We found that combining RNA-seq perturbation-based networks with VIPER (Virtual Inference of Protein Activity by Enriched Regulon analysis) accurately captures splicing factor activation as modulated by multiple regulatory layers. This approach integrates splicing factor regulation into a single score derived solely from exon inclusion signatures, allowing functional interpretation of heterogeneous conditions. As a proof of concept, we identify recurrent cancer splicing programs, revealing oncogenic- and tumor suppressor-like splicing factors missed by conventional methods. These programs correlate with patient survival and key cancer hallmarks: initiation, proliferation, and immune evasion. Altogether, we show splicing factor activity can be accurately estimated from exon inclusion changes, enabling comprehensive analyses of splicing regulation with minimal data requirements.

VIPER↗

PubMed2025

FoldX force field revisited, an improved version.

MOTIVATION: The FoldX force field was originally validated with a database of 1000 mutants at a time when there were few high-resolution structures. Here, we have manually curated a database of 5556 mutants affecting protein stability, resulting in 2484 highly confident mutations denominated FoldX stability dataset (FSD), represented in non-redundant X-ray structures with <2.5 Å resolution, not involving duplicates, metals, or prosthetic groups. Using this database, we have created a new version of the FoldX force field by introducing pi stacking, pH dependency for all charged residues, improving aromatic-aromatic interactions, modifying the Ncap contribution and α-helix dipole, recalibrating the side-chain entropy of methionine, adjusting the H-bond parameters, and modifying the solvation contribution of tryptophan and others. RESULTS: These changes have led to significant improvements for the prediction of specific mutants involving the above residues/interactions and a statistically significant increase of FoldX predictions, as well as for the majority of the 20 aa. Removing all training sets data from FSD [Validation FoldX Stability Dataset (VFSD) dataset] resulted in improved predictions from R = 0.693 (RMSE = 1.277 kcal/mol) to R = 0.706 (RMSE = 1.252 kcal/mol) when compared with the previously released version. FoldX achieves 95% accuracy considering an error of ±0.85 kcal/mol in prediction and an area under the curve = 0.78 for the VFSD, predicting the sign of the energy change upon mutation. AVAILABILITY AND IMPLEMENTATION: FoldX versions 4.1 and 5.1 are freely available for academics at https://foldxsuite.crg.eu/.

Databases, Protein↗

PubMed2023

Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.

Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.

RNA, Transfer↗

PubMed2007

Characterization of vine shoots, cotton stalks, Leucaena leucocephala and Chamaecytisus proliferus, and of their ethyleneglycol pulps.

We characterized vine shoots, cotton stalks, Leucaena leucocephala and Chamaecytisus proliferus as pulping raw materials and found C. proliferus and cotton stalks to be the best for the intended purpose on the grounds of their increased contents in holocellulose (79.73% and 72.86%) and alpha-cellulose (45.37% and 58.48%), and their decreased contents in ethanol-benzene extractables (2.64% and 1.42%), hot water solubles (2.79% and 3.33%) and 1% soda solubles (16.67% and 20.34%). These properties resulted in increased pulp yields and hence in efficient use of these two types of raw material. The previous raw materials were pulped by using an ethyleneglycol concentration of 65% at 180 degrees C for 75min, followed by beating at 1500 revolutions in a PFI refiner. The paper sheets obtained were characterized and those from C. proliferus found to be the best overall as they exhibited an increased breaking length (4644m), stretch (2.87%), burst index (2.46kN/g) tear index (0.33mNm(2)/g) and brightness (49.92% ISO); in addition C. proliferus pulp was obtained with a high-yield (62.88%). On the other hand, vine shoots provided the poorest results among the studied raw materials.

Ethylene Glycol↗

PubMed2006

From in vivo to in silico biology and back.

The massive acquisition of data in molecular and cellular biology has led to the renaissance of an old topic: simulations of biological systems. Simulations, increasingly paired with experiments, are being successfully and routinely used by computational biologists to understand and predict the quantitative behaviour of complex systems, and to drive new experiments. Nevertheless, many experimentalists still consider simulations an esoteric discipline only for initiates. Suspicion towards simulations should dissipate as the limitations and advantages of their application are better appreciated, opening the door to their permanent adoption in everyday research.

Computational Biology↗

PubMed2006

Increased cytogenetic damage in a zone in transition from agricultural to industrial use: Comprehensive analysis of the micronucleus test in peripheral blood lymphocytes.

A complex situation of chemical exposure has been described in México in a zone that is in transition from rural activities towards intensive industrialization, which has brought environmental pollution: chloroform, methylene chloride, indigo and toluene are some of the pollutants found in the Atoyac and Xochiac rivers. A biomonitoring study was planned in order to establish whether there was a biological effect due to the environmental situation. Communities where leukaemia and thrombocytopenic purpura cases have been reported were included in the study, as well as other communities where such cases have not been described. Three occupations were distinguished, according to chemical exposure: industrial workers, agricultural workers and workers in households, education and commerce. A comprehensive analysis in the micronucleus (MN) test was used to study genotoxicity biomarkers. Two metabolic polymorphisms were determined, namely, glutathione transferase mu1 (GSTM1) and theta1 (GSTT1), which are relevant when oxidative responses are involved. Increased genotoxic damage was found, including cells with >1 MN, >1 chromatin bud, and nucleoplasmic bridges. The genotoxic damage was differentially distributed in the regions studied, being more affected those that are closer to the Atoyac and Xochiac rivers, indicating an effect due to environmental exposure to the contaminants present in the rivers. Further characterization of the exposure regimes in these communities will be done in order to contribute to the alleviation of the health risks that environmental pollution is posing on the inhabitants of this area.

Adult↗

PubMed2006

Design and NMR conformational study of a beta-sheet peptide based on Betanova and WW domains.

A good approach to test our current knowledge on formation of protein beta-sheets is de novo protein design. To obtain a three-stranded beta-sheet mini-protein, we have built a series of chimeric peptides by taking as a template a previously designed beta-sheet peptide, Betanova-LLM, and incorporating N- and/or C-terminal extensions taken from WW domains, the smallest natural beta-sheet domain that is stable in absence of disulfide bridges. Some Betanova-LLM strand residues were also substituted by those of a prototype WW domain. The designed peptides were cloned and expressed in Escherichia coli. The ability of the purified peptides to adopt beta-sheet structures was examined by circular dichroism (CD). Then, the peptide showing the highest beta-sheet population according to the CD spectra, named 3SBWW-2, was further investigated by 1H and 13C NMR. Based on NOE and chemical shift data, peptide 3SBWW-2 adopts a well defined three-stranded antiparallel beta-sheet structure with a disordered C-terminal tail. To discern between the contributions to beta-sheet stability of strand residues and the C-terminal extension, the structural behavior of a control peptide with the same strand residues as 3SBWW-2 but lacking the C-terminal extension, named Betanova-LYYL, was also investigated. beta-Sheet stability in these two peptides, in the parent Betanova-LLM and in WW-P, a prototype WW domain, decreased in the order WW-P > 3SBWW-2 > Betanova-LYYL > Betanova-LLM. Conclusions about the contributions to beta-sheet stability were drawn by comparing structural properties of these four peptides.

Amino Acid Sequence↗

PubMed2006

Noise in transcription negative feedback loops: simulation and experimental analysis.

Negative feedback loops have been invoked as a way to control and decrease transcriptional noise. Here, we have built three circuits to test the effect of negative feedback loops on transcriptional noise of an autoregulated gene encoding a transcription factor (TF) and a downstream gene (DG), regulated by this TF. Experimental analysis shows that self-repression decreases noise compared to expression from a non-regulated promoter. Interestingly enough, we find that noise minimization by negative feedback loop is optimal within a range of repression strength. Repression values outside this range result in noise increase producing a U-shaped behaviour. This behaviour is the result of external noise probably arising from plasmid fluctuations as shown by simulation of the network. Regarding the target gene of a self-repressed TF (sTF), we find a strong decrease of noise when repression by the sTF is strong and a higher degree of noise anti-correlation between sTF and its target. Simulations of the circuits indicate that the main source of noise in these circuits could come from plasmid variation and therefore that negative feedback loops play an important role in suppressing both external and internal noise. An important observation is that DG expression without negative feedback exhibits bimodality at intermediate TF repression values. This bimodal behaviour seems to be the result of external noise as it can only be found in those simulations that include plasmid variation.

Computer Simulation↗

PubMed2006

Domain swapping in p13suc1 results in formation of native-like, cytotoxic aggregates.

The field of protein aggregation has been occupied mainly with the study of beta-strand self-association that occurs as a result of misfolding and leads to the formation of toxic protein aggregates and amyloid fibers. However, some of these aggregates retain native-like structural and enzymatic properties suggesting mechanisms other than beta-strand assembly. p13suc1 is a small protein that can exist as a monomer or a domain-swapped dimer. Here, we show that, under native conditions, p13suc1 forms three-dimensional domain-swapped aggregates, and that these aggregates are cytotoxic. Thus, toxicity of protein aggregates is not only associated with beta-rich assemblies and amyloid fibers, involving non-native interactions, but it can be induced by oligomeric misassembly that maintains predominantly native-like interactions.

Animals↗

PubMed2006

Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potential anticancer drug that selectively induces apoptosis in a variety of cancer cells by interacting with death receptors DR4 and DR5. TRAIL can also bind to decoy receptors (DcR1, DcR2, and osteoprotegerin receptor) that cannot induce apoptosis. The occurrence of DR5-responsive tumor cells indicates that a DR5 receptor-specific TRAIL variant will permit tumor-selective therapies. By using the automatic design algorithm FOLD-X, we successfully generated DR5-selective TRAIL variants. These variants do not induce apoptosis in DR4-responsive cell lines but show a large increase in biological activity in DR5-responsive cancer cell lines. Even wild-type TRAIL-insensitive ovarian cancer cell lines could be brought into apoptosis. In addition, our results demonstrate that there is no requirement for antibody-mediated cross-linking or membrane-bound TRAIL to induce apoptosis through DR5.

Apoptosis↗

PubMed2006

Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6.

Formation of multiprotein complexes is a common theme to pattern a cell, thereby generating spatially and functionally distinct entities at specialised regions. Central components of these complexes are scaffold proteins, which contain several protein-protein interaction domains and provide a platform to recruit a variety of additional components. There is increasing evidence that protein complexes are dynamic structures and that their components can undergo various interactions depending on the cellular context. However, little is known so far about the factors regulating this behaviour. One evolutionarily conserved protein complex, which can be found both in Drosophila and mammalian epithelial cells, is composed of the transmembrane protein Crumbs/Crb3 and the scaffolding proteins Stardust/Pals1 and DPATJ/PATJ, respectively, and localises apically to the zonula adherens. Here we show by in vitro analysis that, similar as in vertebrates, the single PDZ domain of Drosophila DmPar-6 can bind to the four C-terminal amino acids (ERLI) of the transmembrane protein Crumbs. To further evaluate the binding capability of Crumbs to DmPar-6 and the MAGUK protein Stardust, analysis of the PDZ structural database and modelling of the interactions between the C-terminus of Crumbs and the PDZ domains of these two proteins were performed. The results suggest that both PDZ domains bind Crumbs with similar affinities. These data are supported by quantitative yeast two-hybrid interactions. In vivo analysis performed in cell cultures and in the Drosophila embryo show that the cytoplasmic domain of Crumbs can recruit DmPar-6 and DaPKC to the plasma membrane. The data presented here are discussed with respect to possible dynamic interactions between these proteins.

Animals↗

PubMed2006

Protein aggregation and amyloidosis: confusion of the kinds?

Recent years have witnessed major advances in our understanding of the structural basis of protein aggregation on several fronts. Firstly, high-resolution structural information that remained elusive for many years was provided by a series of studies of amyloid fibers using NMR, X-ray crystallography and electron microscopy, thereby confirming earlier models based on lower resolution observations. Secondly, studies of the sequence determinants of protein aggregation culminated in the development of computer algorithms that predict aggregation-prone sequences with good accuracy, allowing the design of mutations that reduce aggregation. Thirdly, based on the first results from such predictions and on statistical analysis of naturally occurring aggregating sequences, a picture is emerging in which aggregation-prone sequences are capped by gatekeeper residues that oppose aggregation. In addition to their aggregation-opposing function, it seems that gatekeeper residues are also important in determining chaperone selectivity for strongly aggregating regions. Finally, recent computational and experimental work shows that preventing aggregation does not necessarily mean that amyloid formation is prevented and vice versa. Thus, although aggregation and amyloidosis correlate to a certain extent, they are different processes and should be treated as such.

Algorithms↗

PubMed2006

Synthetic biology: challenges ahead.

Explore the source record for details and available documents.

Biomimetics↗

PubMed2006

New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae.

SH3 domains are small protein modules that are involved in protein-protein interactions in several essential metabolic pathways. The availability of the complete genome and the limited number of clearly identifiable SH3 domains make the yeast Saccharomyces cerevisae an ideal proteomic-based model system to investigate the structural rules dictating the SH3-mediated protein interactions and to develop new tools to assist these studies. In the present work, we have determined the solution structure of the SH3 domain from Myo3 and modeled by homology that of the highly homologous Myo5, two myosins implicated in actin polymerization. We have then implemented an integrated approach that makes use of experimental and computational methods to characterize their binding properties. While accommodating their targets in the classical groove, the two domains have selectivity in both orientation and sequence specificity of the target peptides. From our study, we propose a consensus sequence that may provide a useful guideline to identify new natural partners and suggest a strategy of more general applicability that may be of use in other structural proteomic studies.

Binding Sites↗

PubMed2006

Prediction of protein-protein interaction based on structure.

A great challenge in the proteomics and structural genomics era is to predict protein structure and function from sequence, including the identification of biological partners. The development of a procedure to construct position-specific scoring matrices for the prediction and identification of sequences with putative significant affinity faces this challenge. The local and web applications used for sequence and structure search, sequence alignment, protein modeling, molecule edition and modification, and scoring matrices construction are described in detail. The methodology is based on the information contained in structural databases and takes into account the subtle conformational and sequence details that characterize different structures within a family. Using the matrices, the protein sequence databases can be easily scanned to locate putative partners of biological significance. The success of this methodology opens the way for the prediction of protein-protein interaction at genome scale.

Algorithms↗

PubMed2006

Standards for medical device communication: X73 PoC-MDC.

When using a number of medical devices from very different manufacturers with different proprietary formats the problem of a lack of interoperability emerges. Connectivity and communications are then limited and the systems and users can not exploit all the possibilities that Information and Communication Technologies offer today. The use and application of standards can be the solution to bring light to this confusion of languages in this Tower of Babel. There are several standards applicable to medical information systems interoperability and, analyzing these different options, the X73 PoC-MDC (ISO11073/IEEE1073) set of standards for Point of Care Medical Device Communication is the best positioned international standard to provide interoperability in these communications.

Computer Communication Networks↗

PubMed2005

How evolutionary pressure against protein aggregation shaped chaperone specificity.

As protein aggregation is potentially lethal, control of protein conformation by molecular chaperones is essential for cellular organisms. This is especially important during protein expression and translocation, since proteins are then unfolded and therefore most susceptible to form non-native interactions. Using TANGO, a statistical mechanics algorithm to predict protein aggregation, we here analyse the aggregation propensities of 28 complete proteomes. Our results show that between 10% and 20% of the residues in these proteomes are within aggregating protein segments and that this represents a lower limit for the aggregation tendency of globular proteins. Further, we show that not only evolution strongly pressurizes aggregation downwards by minimizing the amount of strongly aggregating sequences but also by selectively capping strongly aggregating hydrophobic protein sequences with arginine, lysine and proline. These residues are strongly favoured at these positions as they function as gatekeepers that are most efficient at opposing aggregation. Finally, we demonstrate that the substrate specificity of different unrelated chaperone families is geared by these gatekeepers. Chaperones face the difficulty of having to combine substrate affinity for a broad range of hydrophobic sequences and selectivity for those hydrophobic sequences that aggregate most strongly. We show that chaperones achieve these requirements by preferentially binding hydrophobic sequences that are capped by positively charged gatekeeper residues. In other words, targeting evolutionarily selected gatekeepers allows chaperones to prioritize substrate recognition according to aggregation propensity.

Algorithms↗