A5036217074- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced Electron Microscopy Techniques and Applications
- Electron and X-Ray Spectroscopy Techniques
- RNA and protein synthesis mechanisms
- X-ray Spectroscopy and Fluorescence Analysis
- Force Microscopy Techniques and Applications
- Heat shock proteins research
- Galectins and Cancer Biology
- Microfluidic and Bio-sensing Technologies
- Erythrocyte Function and Pathophysiology
- Mass Spectrometry Techniques and Applications
- Quantum Dots Synthesis And Properties
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- bioluminescence and chemiluminescence research
- Particle Detector Development and Performance
- Gene Regulatory Network Analysis
- Photocathodes and Microchannel Plates
- Biochemical and Structural Characterization
- Monoclonal and Polyclonal Antibodies Research
- Mobile and Web Applications
- Photosynthetic Processes and Mechanisms
- Chemical Synthesis and Analysis
- RNA modifications and cancer
Scripps Institution of Oceanography
2020-2025
Scripps (United States)
2021-2024
La Jolla Alcohol Research
2024
University of Washington
2016-2022
Seattle University
2019-2022
Scripps Research Institute
2020
Fundación Ciencias Exactas y Naturales
2017
University of Buenos Aires
2017
Designing proteins with cavities In de novo protein design, creating custom-tailored binding sites is a particular challenge because these often involve nonideal backbone structures. For example, curved b sheets are common ligand motif. Marcos et al. investigated the principles that drive β-sheet curvature by studying geometry of β in natural and folding simulations. step toward custom design enzyme catalysts, they used to control differently shaped cavities. Science , this issue p. 201
Significance Reengineering naturally occurring proteins to have new functions has had considerable impact on industrial and biomedical applications, but is limited by the finite number of known proteins. A promise de novo protein design generate a larger more diverse set structures than currently available. This vision not yet been realized for small-molecule binder or enzyme due complexity pocket-containing structures. Here we present an algorithm that systematically generates NTF2-like...
Small heat shock proteins (sHSPs) are nature's 'first responders' to cellular stress, interacting with affected prevent their aggregation. Little is known about sHSP structure beyond its structured α-crystallin domain (ACD), which flanked by disordered regions. In the human HSPB1, N-terminal region (NTR) represents nearly 50% of sequence. Here, we present a hybrid approach involving NMR, hydrogen-deuterium exchange mass spectrometry, and modeling provide first residue-level characterization...
Transthyretin (TTR) is a natively tetrameric thyroxine transporter found in blood and cerebrospinal fluid whose misfolding aggregation causes transthyretin amyloidosis. A rational drug design campaign identified the small molecule tafamidis (Vyndaqel/Vyndamax) as an effective stabilizer of native TTR fold, this inhibitor regulatory agency-approved for treatment Despite 50 years structural studies on triumph structure-based design, there remains notable dearth information available to...
Developments in direct electron detector technology have played a pivotal role enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory recent experiments indicate advantages to imaging 100 keV, energies for which the current detectors not been optimized. In this study, we evaluated Gatan Alpine detector, designed operation Compared K3, demonstrated significant DQE improvement these energies, specifically ∼ 4-fold Nyquist single-particle experiments, datasets...
Abstract While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated an exciting alternative. Here we explore the customization backbone designed eight stranded β‐barrel protein create catalysts retro‐aldolase model reaction. We show that active specific can be this fold use directed evolution further optimize activity stereoselectivity. Our results support...
Abstract The diversity and flexibility of life offers a wide variety molecules systems useful for biosensing. A biosensor device should be robust, specific reliable. Inorganic arsenic is highly toxic water contaminant with worldwide distribution that poses threat to public health. With the goal developing an biosensor, we designed incoherent feed-forward loop (I-FFL) genetic circuit correlate its output pulse input signal in relatively time-independent manner. system was conceived...
Cryogenic electron microscopy (cryoEM) has emerged as a powerful technique for probing the atomic structure of macromolecular complexes. Sample preparation cryoEM requires preserving specimens in thin layer vitreous ice, typically suspended within holes fenestrated support film. However, all commonly used sample approaches studies expose specimen to air-water interface, introducing strong hydrophobic effect on that often results denaturation, aggregation, and complex dissociation. Further,...
Critical molecular events that control conformational transitions in most allosteric proteins are ill-defined. The mannose-specific FimH protein of Escherichia coli is a prototypic bacterial adhesin switches from an ‘inactive’ low-affinity state (LAS) to ‘active’ high-affinity (HAS) conformation allosterically upon mannose binding and mediates shear-dependent catch bond adhesion. Here we identify novel type antibody acts as kinetic trap prevents the transition between conformations both...
ABSTRACT Developments in direct electron detector technology have played a pivotal role enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory recent experiments indicate advantages to imaging 100 keV, energies for which the current detectors not been optimized. In this study, we evaluated Gatan Alpine detector, designed operation Compared K3, demonstrated significant DQE improvement these voltages, specifically ~4-fold Nyquist single-particle experiments,...
Buffer-composition and sample-preparation guidelines for cryo-electron microscopy are geared towards maximizing imaging contrast reducing electron-beam-induced motion. These pursuits often involve the minimization or complete removal of additives that commonly used to facilitate proper protein folding minimize aggregation. Among these admonished is glycerol, a widely osmolyte aids stability. In this work, it shown inclusion glycerol does not preclude high-resolution structure determination...
Abstract Design of polar interactions is a current challenge for protein design. The de novo designed Top7, like almost all proteins, has an entirely nonpolar core. Here we describe the replacing sizable fraction (5 residues) this core with hydrogen bond network. design expressed at high levels in E. coli , folding free energy 10 kcal/mol, and retains multiphasic kinetics original Top7. NMR structure shows that conformations three five residues, bonds between them, are very close to those...
Cryo-electron tomography is a powerful biophysical technique enabling three-dimensional visualization of complex biological systems. Macromolecular targets interest identified within cryo-tomograms can be computationally extracted, aligned, and averaged to produce better-resolved structure through process called subtomogram averaging (STA). However, accurate alignment macromolecular machines that exhibit extreme structural heterogeneity conformational flexibility remains significant...
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Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing high-resolution insights into biological macromolecules. Here, we present sub-3 Å resolution structures determined using the 100 keV Tundra cryogenic transmission electron microscope (cryo-TEM), equipped with newly developed Falcon C direct detector (DED). Our results demonstrate that this lower voltage microscope, when combined advanced optics and detectors, can achieve reconstructions were previously only...
ABSTRACT Small heat shock proteins (sHPSs) are nature’s “first responders” to cellular stress, interacting with affected prevent their aggregation. Little is known about sHSP structure beyond its structured α-crystallin domain (ACD), which flanked by disordered regions. In the human HSPB1, N-terminal region (NTR) represents nearly 50% of sequence. Here, we present a hybrid approach involving NMR, hydrogen-deuterium exchange mass spectrometry, and modeling provide first residue-level...
Abstract Buffer composition and sample preparation guidelines for cryo-electron microscopy are geared toward maximizing imaging contrast reducing electron beam-induced motion. These pursuits often involve the minimization or complete removal of additives that commonly used to facilitate proper protein folding minimize aggregation. Among these admonished is glycerol, a widely osmolyte aids stability. In this work, we show inclusion glycerol does not preclude high-resolution structure...
Cryogenic electron microscopy (cryoEM) has emerged as a powerful technique for probing the atomic structure of macromolecular complexes. Sample preparation cryoEM requires preserving specimens in thin layer vitreous ice, typically suspended within holes fenestrated support film. However, all commonly used sample approaches studies expose specimen to air-water interface, introducing strong hydrophobic effect on that often results denaturation, aggregation, and complex dissociation. Further,...