A5006882336- Protein Structure and Dynamics
- Antibiotic Resistance in Bacteria
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Enzyme Catalysis and Immobilization
- Photosynthetic Processes and Mechanisms
- Glycosylation and Glycoproteins Research
- Vibrio bacteria research studies
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Carbohydrate Chemistry and Synthesis
- Yersinia bacterium, plague, ectoparasites research
- Protein Tyrosine Phosphatases
- Innovative Microfluidic and Catalytic Techniques Innovation
- Redox biology and oxidative stress
- Enzyme Production and Characterization
- Enzyme-mediated dye degradation
- Galectins and Cancer Biology
- Gut microbiota and health
- Peptidase Inhibition and Analysis
- bioluminescence and chemiluminescence research
- Biochemical and Molecular Research
- Microtubule and mitosis dynamics
Universidad de Granada
2016-2025
Geoambiente (Brazil)
2025
National University of Quilmes
2004-2019
Instituto Multidisciplinario de Biología Celular
2012
Consejo Nacional de Investigaciones Científicas y Técnicas
2004-2011
Centro Científico Tecnológico - San Juan
2005
University of Buenos Aires
2004
We report a sequence reconstruction analysis targeting several Precambrian nodes in the evolution of class-A β-lactamases and preparation experimental characterization their encoded proteins. Despite extensive differences with modern enzymes (~100 amino acid differences), proteins resurrected laboratory properly fold into canonical lactamase structure. The from 2-3 billion years (Gyr)-old β-lactamase sequences undergo cooperative two-state thermal denaturation display very large temperature...
β-lactamases are produced by many modern bacteria as a mechanism of resistance toward β-lactam antibiotics, the most common antibiotics in use. β-lactamases, however, ancient enzymes that originated billions years ago. Recently, proteins corresponding to 2- 3-Gy-old Precambrian nodes evolution Class A have been prepared and shown be moderately efficient promiscuous catalysts, able degrade variety with catalytic efficiency levels similar those an average enzyme. Remarkably, there few...
Abstract TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes degraded variety of moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting role dynamics in enzyme evolution. Here, we develop conformational computational approach rationally mold protein flexibility profile on...
Enzymes are the quintessential green catalysts, but realizing their full potential for biotechnology typically requires improvement of biomolecular properties. Catalysis enhancement, however, is often accompanied by impaired stability. Here, we show how interplay between activity and stability in enzyme optimization can be efficiently addressed coupling two recently proposed methodologies guiding directed evolution. We first identify catalytic hotspots from chemical shift perturbations...
Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different acid. It has been recently debated whether these remain approximately constant during evolution or whether, due to coevolution sites, they change strongly. Such research highlights an unresolved fundamental issue with far-reaching implications phylogenetic analysis molecular modeling. Here, we take advantage the...
Abstract Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in last universal common ancestor. Mechanisms for active sites must therefore either plausibly exist or at least have existed primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds and demonstrate that a site can generated through single hydrophobic-to-ionizable amino...
ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTManipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic FunctionsJasmine M. GardnerJasmine GardnerDepartment of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, SwedenMore by Jasmine Gardner, Michal BilerMichal BilerDepartment Biler, Valeria A. RissoValeria RissoDepartamento de Quı́mica Fisica, Facultad Ciencias, Unidad Excelencia Aplicada a Biomedicina y Medioambiente (UEQ), Universidad Granada, 18071...
Consensus-sequence engineering has generated protein variants with enhanced stability, and sometimes, modulated biological function. Consensus mutations are often interpreted as the introduction of ancestral amino acid residues. However, precise relationship between consensus resurrection is not fully understood. Here, we report properties proteins encoded by sequences derived from a multiple sequence alignment extant, class A β-lactamases, compared ancient Precambrian β-lactamases...
Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains sluggish, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib is a novel approach which uses phylogenetic analysis Rosetta design rank variants with multiple mutations, on the basis predicted stability. Here, we use it target active site region minimalist-designed, de novo Kemp eliminase. The...
Among the broad repertory of protein engineering methods that set out to improve stability, consensus design has proved be a powerful strategy stabilize enzymes without compromising their catalytic activity. Here, we have applied an in-house method laboratory evolved high-redox potential laccase. Multiple sequence alignments were carried and computationally refined by applying relative entropy mutual information thresholds. Through this approach, ensemble 20 mutations identified, 18 which...
Abstract Glycosidases are phylogenetically widely distributed enzymes that crucial for the cleavage of glycosidic bonds. Here, we present exceptional properties a putative ancestor bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares TIM-barrel fold with its modern descendants but displays large regions greatly enhanced conformational flexibility. Yet, barrel core remains comparatively rigid glycosidase activity is stable, an optimum temperature within experimental...
Ancestral sequence reconstruction and resurrection provides useful information for protein engineering, yet its alliance with directed evolution has been little explored. In this study, we have resurrected several ancestral nodes of fungal laccases dating back ∼500 to 250 million years. Unlike modern laccases, the Mesozoic were readily secreted by yeast, similar kinetic parameters, a broader stability, distinct pH activity profiles. The Agaricomycetes laccase carried 136 mutations, molecular...
We discuss the unique properties found and new exciting possibilities implicit in recent laboratory resurrections of Precambrian proteins.
Rubisco is an ancient, catalytically conserved yet slow enzyme, which plays a central role in the biosphere's carbon cycle. The design of Rubiscos to increase agricultural productivity has hitherto relied on use vivo selection systems, precluding exploration biochemical traits that are not wired cell survival. We present directed -in vitro- evolution platform extracts enzyme from its biological context provide new avenue for engineering. Precambrian and extant form II were subjected ensemble...
Many experimental analyses and proposed scenarios support that ancient life was thermophilic. In congruence with this hypothesis, proteins encoded by reconstructed sequences corresponding to phylogenetic nodes often display very high stability. Here, we show such 'reconstructed ancestral hyperstability' can be further engineered on the basis of a straightforward approach uses exclusively information afforded reconstruction process itself. Since evolution does not imply continuous...
Abstract Protein sequence space is vast. This fact, together with the prevalence of epistasis, hampers engineering novel enzymes through library screening and a major obstacle to any attempt predict natural protein evolution. Recently, specialized methodologies have been used determine fitness data on ∼260000 sequences for gene enzyme dihydrofolate reductase antibody affinity all combinations mutations present in receptor binding domain (RBD) Omicron strain SARS-CoV-2 (∼30000 variants). We...
Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity these is regulated by the motion catalytic loop places critical conserved aspartic acid side chain into active site for acid-base catalysis upon closure. These also have phosphate binding typically highly rigid and forms well-defined anion nest. intimate links between dynamics chemistry make PTPs an excellent model system understanding role protein...
The protein sequence space is vast. This fact, together with the prevalence of epistasis, hampers engineering novel enzymes through library screening and a major obstacle to any attempt predict natural evolution. Recently, specialized methodologies have been used determine fitness data on ~260,000 sequences for gene enzyme dihydrofolate reductase antibody affinity all combinations mutations present in receptor-binding domain (RBD) Omicron strain SARS-CoV-2 (~30,000 variants). We show that...
The relationship between the denaturation temperatures of proteins (Tm values) and living their host organisms (environmental temperatures: TENV is poorly understood. Since different in same organism may show widely Tm's, no simple universal Tm should hold, other than Tm≥TENV. Yet, when analyzing a set homologous from hosts, Tm's are oftentimes found to correlate with TENV's but this correlation shifted upward on axis. Supporting trend, we recently reported for resurrected Precambrian...