Research Group

Detalle de: Synthetic Structural Biology

Title	Synthetic Structural Biology
Description	The Synthetic Structural Biology Lab, led by Ulrich Eckhard, is a dynamic research group at the IBMB-CSIC. Supported by the Ramon y Cajal Program (2022-2027), we’re exploring the exciting intersection of structural biochemistry, synthetic microbiology, and enzyme engineering. We’re particularly focused on: Understanding proteolytic flagellins: Uncovering their structural basis, biological role in biofilm remodeling and pathogenesis, and impact on bacterial lifestyle. Reprogramming of bacterial flagella: Engineering structural flagellins to encode enzymatic units and developing these augmented bacteria for biotechnological and biomedical applications. Enzyme Engineering and Design: Using computational approaches and structural insights to engineer and design enzymes with tailored functionalities. Our lab is a collaborative, international training environment, and we actively welcome Erasmus+, Bachelor, and Master students. If you are interested in joining us – or if you are interested in applying for competitive third-party funding for PhD and post-doc projects – please get in touch!
Home Page	https://ibmb.csic.es/en/department-of-structural-and-molecular-biology/synthetic-structural-biology/
Contact Email	ulrich.eckhard@ibmb.csic.es
Collaborating Companies
Spin Off
Patents
Hpc Resources
Institution	IBMB
Ontology	Computational Methods, Applications of Computational Biology, Structural bioinformatics, Experimental structure determination, Computational models and simulations, Mutation Analysis and design, Proteomics, Biomolecular simulation, Drug Discovery and design, Structure prediction, Molecular Interactions/Docking, Protein/Nucleic Acid design
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Service Units
Research Lines	Proteolytic flagellins, Reprogramming of bacterial flagella, Enzyme engineering and design, Structural biochemistry of proteolytic enzymes and their inhibitors
Funded Projects	IgA-cleaving Peptidases: Allies and Adversaries in Biotechnology, Biomedicine, and Infection (IgA-PEP), Revolutionizing Protein Drug Development – AI-driven Protein Engineering for Next-Generation Enzyme Therapy, Redesigning bacterial flagella to harbor functional domains for biotechnology and biomedicine, Diseño de proteínas basado en IA unido a tecnologías moleculares avanzadas para el desarrollo, investigación y mejora de VLPs de nueva generación para terapias avanzadas, Structural and Computational Biochemistry of Proteins (BIOSTROMP), Structural Biochemistry of Proteolytic Enzymes
Selected Publications	Computational Insights into Membrane Disruption by Cell-Penetrating Peptides Article · 17 Jan 2025 Decoding the molecular and structural determinants of the neurokinin A and Aβ1-42 peptide cross-interaction in the amyloid cascade pathway Article · Nov 2024 Structural and functional insights into the C-terminal signal domain of the Bacteroidetes type-IX secretion system Article · Jun 2024 Conditional language models enable the efficient design of proficient enzymes Preprint · 5 May 2024 Experimental and computational biophysics to identify vasodilator drugs targeted at TRPV2 using agonists based on the probenecid scaffold Article · 2 Jan 2024 View all (46 more) Advanced Binary Guanosine and Guanosine 5'-Monophosphate Cell-Laden Hydrogels for Soft Tissue Reconstruction by 3D Bioprinting Article · 15 Jun 2023 Structural insights into latency of the metallopeptidase ulilysin (lysargiNase) and its unexpected inhibition by a sulfonyl–fluoride inhibitor of serine peptidases Article · 2023 A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia Article · 2023 De novo design of immunoglobulin-like domains Article · 3 Oct 2022 Repositioning small molecule drugs as allosteric inhibitors of the BFT-3 toxin from enterotoxigenic Bacteroides fragilis Article · 27 Sep 2022 Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy Article · 1 Aug 2022 In Silico Assessment of the Lipid Fingerprint Signature of ATP2, the Essential P4-ATPase of Malaria Parasites Article · 12 Jul 2022 An Introduction to Bacterial Biofilms and Their Proteases, and Their Roles in Host Infection and Immune Evasion Article · 14 Feb 2022 An engineered protein-based submicromolar competitive inhibitor of the Staphylococcus aureus virulence factor aureolysin Article · Jan 2022 Proteolytic Profiling of Streptococcal Pyrogenic Exotoxin B (SpeB) by Complementary HPLC-MS Approaches Article · 30 Dec 2021 Antibacterial approaches in tissue engineering using metal ions and nanoparticles: From mechanisms to applications Article · Dec 2021 Intermolecular latency regulates the essential C-terminal signal peptidase and sortase of the secretion Article · 30 Sep 2021 The crystal structure of a 250-kDa heterotetrameric particle explains inhibition of sheddase meprin β by endogenous fetuin-B Article · 29 Mar 2021 AbaM Regulates Quorum Sensing, Biofilm Formation, and Virulence in Acinetobacter baumannii Article · 23 Mar 2021 Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring—An Inactive Enzyme with Intact Substrate Binding Article · 3 Dec 2020 Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis Article · 4 Nov 2020 Quorum Sensing in Acinetobacter Virulence Book / chapter · Jan 2020 C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease Article · 20 Jun 2018 Melanocyte development in the mouse tail epidermis requires the Adamts9 metalloproteinase Article · 5 Jun 2018 A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function Article · 28 May 2018 TAILS N-terminomics and proteomics reveal complex regulation of proteolytic cleavage by O-glycosylation Article · May 2018 Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification Article · 21 Dec 2017 The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes Article · 16 Oct 2017 Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella Article · 12 Sep 2017 Degradomic and yeast 2-hybrid inactive catalytic domain substrate trapping identifies new membrane-type 1 matrix metalloproteinase (MMP14) substrates: CCN3 (Nov) and CCN5 (WISP2) Article · May 2017 TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors Article · Aug 2016 Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14 Article · Jun 2016 Positional proteomics in the era of the human proteome project on the doorstep of precision medicine Article · Mar 2016 Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses Article · Jan 2016 TAILS N-terminomic and proteomic datasets of healthy human dental pulp Article · Dec 2015 The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues Article · 10 Aug 2015 Protein Termini and Their Modifications Revealed by Positional Proteomics Article · 4 Jun 2015 TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage Article · 18 Dec 2014 LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification Article · 24 Nov 2014 Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries Article · 11 Sep 2014 Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen Article · Apr 2014 Role of Acinetobacter baumannii UmuD Homologs in Antibiotic Resistance Acquired through DNA Damage-Induced Mutagenesis Article · Mar 2014 Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity Article · 20 Dec 2013 Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T Article · Jul 2013 Systems-Level Analysis of Proteolytic Events in Increased Vascular Permeability and Complement Activation in Skin Inflammation Article · 15 Jan 2013 Crystallographically Mapped Ligand Binding Differs in High and Low IgE Binding Isoforms of Birch Pollen Allergen Bet v 1 Article · Sep 2012 Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis Article · 25 Sep 2011 Polycystic kidney disease-like domains of clostridial collagenases and their role in collagen recruitment Article · 28 Aug 2011 A universal strategy for high-yield production of soluble and functional clostridial collagenases in E. coli Article · 31 Mar 2009 Biochemical characterization of the catalytic domains of three different clostridial collagenases Article · 21 Oct 2008 Crystallization and preliminary X-ray characterization of the catalytic domain of collagenase G from Clostridium histolyticum Article · 24 Apr 2008
Researchers	Mario López Martín, Ulrich Eckhard

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