Search results for: Eva Nogales

Items from 1 to 20 out of 84 results

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Towards a mechanistic understanding of core promoter recognition from cryo-EM studies of human TFIID

Eva Nogales, Avinash B Patel, Robert K Louder

Current Opinion in Structural Biology > 2017 > 47 > C > 60-66

TFIID is a critical component of the eukaryotic transcription pre-initiation complex (PIC) required for the recruitment of RNA Pol II to the start site of protein-coding genes. Within the PIC, TFIID's role is to recognize and bind core promoter sequences and recruit the rest of the PIC components. Due to its size and its conformational complexity, TFIID poses a serious challenge for structural characterization...

article

How Cryo-EM Became so Hot

Yifan Cheng, Robert M. Glaeser, Eva Nogales

Cell > 2017 > 171 > 6 > 1229-1231

The Royal Swedish Academy of Sciences awarded the 2017 Nobel Prize for Chemistry to Jacques Dubochet, Joachim Frank, and Richard Henderson for “developing cryoelectron microscopy for the high-resolution structure determination of biomolecules in solution.” Achieving this goal, which required innovation, persistence, and uncommon physical insight, has broadened horizons for structural studies in molecular...

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Challenges and opportunities in the high-resolution cryo-EM visualization of microtubules and their binding partners

Eva Nogales, Elizabeth H Kellogg

Current Opinion in Structural Biology > 2017 > 46 > C > 65-70

As non-crystallizable polymers, microtubules have been the target of cryo-electron microscopy (cryo-EM) studies since the technique was first established. Over the years, image processing strategies have been developed that take care of the unique, pseudo-helical symmetry of the microtubule. With recent progress in data quality and data processing, cryo-EM reconstructions are now reaching resolutions...

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Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures

Elizabeth H. Kellogg, Nisreen M.A. Hejab, Stuart Howes, Peter Northcote, more

Journal of Molecular Biology > 2017 > 429 > 5 > 633-646

A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9–4.2Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct,...

article

Effects of Bni5 Binding on Septin Filament Organization

Elizabeth A. Booth, Sarah M. Sterling, Dustin Dovala, Eva Nogales, more

Journal of Molecular Biology > 2016 > 428 > 24(PB) > 4962-4980

Septins are a protein family found in all eukaryotes (except higher plants) that have roles in membrane remodeling and formation of diffusion barriers and as a scaffold to recruit other proteins. In budding yeast, proper execution of cytokinesis and cell division requires the formation of a collar of circumferential filaments at the bud neck. These filaments are assembled from apolar septin hetero-octamers...

article

Next-generation electron microscopy in autophagy research

James H Hurley, Eva Nogales

Current Opinion in Structural Biology > 2016 > 41 > C > 211-216

Autophagy is the process whereby cytosol, organelles, and inclusions are taken up in a double-membrane vesicle known as the autophagosome, and transported to the lysosome for destruction and recycling. Electron microscopy (EM) led to the discovery of autophagy in the 1950s and has been a central part of its characterization ever since. New capabilities in single particle EM studies of the autophagy...

article

Cryo-EM in the study of challenging systems: the human transcription pre-initiation complex

Eva Nogales, Robert K Louder, Yuan He

Current Opinion in Structural Biology > 2016 > 40 > C > 120-127

Single particle cryo-Electron Microscopy (cryo-EM) is a technique that allows the structural characterization of macromolecules without the need for crystallization. For certain type of samples that are ideally suited for cryo-EM studies it has been possible to reach high-resolution structures following relatively standard procedures. Other biological systems remain highly challenging, even for cryo-EM...

article

DNA Targeting by a Minimal CRISPR RNA-Guided Cascade

Megan L. Hochstrasser, David W. Taylor, Jack E. Kornfeld, Eva Nogales, more

Molecular Cell > 2016 > 63 > 5 > 840-851

Bacteria employ surveillance complexes guided by CRISPR (clustered, regularly interspaced, short palindromic repeats) RNAs (crRNAs) to target foreign nucleic acids for destruction. Although most type I and type III CRISPR systems require four or more distinct proteins to form multi-subunit surveillance complexes, the type I-C systems use just three proteins to achieve crRNA maturation and double-stranded...

article

Mutations in Human Tubulin Proximal to the Kinesin-Binding Site Alter Dynamic Instability at Microtubule Plus- and Minus-Ends

Shih-Chieh Ti, Melissa C. Pamula, Stuart C. Howes, Christian Duellberg, more

Developmental Cell > 2016 > 37 > 1 > 72-84

The assembly of microtubule-based cellular structures depends on regulated tubulin polymerization and directional transport. Here, we purify and characterize tubulin heterodimers that have human β-tubulin isotype III (TUBB3), as well as heterodimers with one of two β-tubulin mutations (D417H or R262H). Both point mutations are proximal to the kinesin-binding site and have been linked to an ocular...

article

Visualizing microtubule structural transitions and interactions with associated proteins

Eva Nogales, Rui Zhang

Current Opinion in Structural Biology > 2016 > 37 > C > 90-96

Microtubules (MTs) have been the subject of cryo-electron microscopy (cryo-EM) studies since the birth of this technique. Although MTs pose some unique challenges, having to do with the presence of a MT seam, lattice variability and disorder, MT cryo-EM reconstructions are steadily improving in resolution and providing exciting new insights into MT structure and function. Recent work has lead to the...

article

An electron microscopy journey in the study of microtubule structure and dynamics

Eva Nogales

Protein Science > 24 > 12 > 1912 - 1919

Structural characterization of microtubules has been the realm of three‐dimensional electron microscopy and thus has evolved hand in hand with the progress of this technique, from the initial 3D reconstructions of stained tubulin assemblies, and the first atomic model of tubulin by electron crystallography of 2D sheets of protofilaments, to the ever more detailed cryoelectron microscopy structures...

article

Protein domain mapping by internal labeling and single particle electron microscopy

Claudio Ciferri, Gabriel C. Lander, Eva Nogales

Journal of Structural Biology > 2015 > 192 > 2 > 159-162

In recent years, electron microscopy (EM) and single particle analysis have emerged as essential tools for investigating the architecture of large biological complexes. When high resolution is achievable, crystal structure docking and de-novo modeling allows for precise assignment of individual protein domain sequences. However, the achievable resolution may limit the ability to do so, especially...

article

A new protocol to accurately determine microtubule lattice seam location

Rui Zhang, Eva Nogales

Journal of Structural Biology > 2015 > 192 > 2 > 245-254

Microtubules (MTs) are cylindrical polymers of αβ-tubulin that display pseudo-helical symmetry due to the presence of a lattice seam of heterologous lateral contacts. The structural similarity between α- and β-tubulin makes it difficult to computationally distinguish them in the noisy cryo-EM images, unless a marker protein for the tubulin dimer, such as kinesin motor domain, is present. We have developed...

article

Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins

Rui Zhang, Gregory M. Alushin, Alan Brown, Eva Nogales

Cell > 2015 > 162 > 4 > 849-859

Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo-electron microscopy (cryo-EM) structures of MTs, at 3.5 Å or better resolution, bound to GMPCPP, GTPγS, or GDP, either decorated with kinesin motor domain after polymerization or copolymerized with EB3...

article

Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity

Eva Nogales, Sjors H.W. Scheres

Molecular Cell > 2015 > 58 > 4 > 677-689

3D cryo-electron microscopy (cryo-EM) is an expanding structural biology technique that has recently undergone a quantum leap progression in its achievable resolution and its applicability to the study of challenging biological systems. Because crystallization is not required, only small amounts of sample are needed, and because images can be classified in a computer, the technique has the potential...

article

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

Raymond H.J. Staals, Yifan Zhu, David W. Taylor, Jack E. Kornfeld, more

Molecular Cell > 2014 > 56 > 4 > 518-530

CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. Here we report the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). TtCsm is composed of five different protein subunits (Csm1–Csm5) with an uneven stoichiometry and a single crRNA of variable size...

article

High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis

Gregory M. Alushin, Gabriel C. Lander, Elizabeth H. Kellogg, Rui Zhang, more

Cell > 2014 > 157 > 5 > 1117-1129

Dynamic instability, the stochastic switching between growth and shrinkage, is essential for microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and is inhibited by anticancer agents like Taxol. We provide insight into the mechanism of dynamic instability, based on high-resolution cryo-EM structures (4.7–5.6 Å) of dynamic microtubules and microtubules stabilized...

article

Dynamic Mechanical Responses of Arabidopsis Thylakoid Membranes during PSII-Specific Illumination

Casper H. Clausen, Matthew D. Brooks, Tai-De Li, Patricia Grob, more

Biophysical Journal > 2014 > 106 > 9 > 1864-1870

Remodeling of thylakoid membranes in response to illumination is an important process for the regulation of photosynthesis. We investigated the thylakoid network from Arabidopsis thaliana using atomic force microscopy to capture dynamic changes in height, elasticity, and viscosity of isolated thylakoid membranes caused by changes in illumination. We also correlated the mechanical response of the thylakoid...

article

Defining the Superfamily Conserved Mechanism for Flap Endonucleases FEN1 and XPG Specificity for 5' Flap DNA and DNA Bubbles, Respectively, by Hybrids Methods of Crystallography, SAXS, EM, and Computation

Susan Tsutakawa, Andrew Arvai, Altaf Sarker, Jordi Querol-Audi, more

Biophysical Journal > 2014 > 106 > 2 Supplement 1 > 230a

article

Dynamic Mechanical Responses of Arabidopsis Thylakoid Membranes during PSII-Specific Illumination

Tai-De Li, Casper Clausen, Matthew Brooks, Patricia Grob, more

Biophysical Journal > 2014 > 106 > 2 Supplement 1 > 181a

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Search results for: Eva Nogales

Towards a mechanistic understanding of core promoter recognition from cryo-EM studies of human TFIID

How Cryo-EM Became so Hot

Challenges and opportunities in the high-resolution cryo-EM visualization of microtubules and their binding partners

Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures

Effects of Bni5 Binding on Septin Filament Organization

Next-generation electron microscopy in autophagy research

Cryo-EM in the study of challenging systems: the human transcription pre-initiation complex

DNA Targeting by a Minimal CRISPR RNA-Guided Cascade

Mutations in Human Tubulin Proximal to the Kinesin-Binding Site Alter Dynamic Instability at Microtubule Plus- and Minus-Ends

Visualizing microtubule structural transitions and interactions with associated proteins

An electron microscopy journey in the study of microtubule structure and dynamics

Protein domain mapping by internal labeling and single particle electron microscopy

A new protocol to accurately determine microtubule lattice seam location

Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins

Cryo-EM: A Unique Tool for the Visualization of Macromolecular Complexity

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

High-Resolution Microtubule Structures Reveal the Structural Transitions in αβ-Tubulin upon GTP Hydrolysis

Dynamic Mechanical Responses of Arabidopsis Thylakoid Membranes during PSII-Specific Illumination

Defining the Superfamily Conserved Mechanism for Flap Endonucleases FEN1 and XPG Specificity for 5' Flap DNA and DNA Bubbles, Respectively, by Hybrids Methods of Crystallography, SAXS, EM, and Computation

Dynamic Mechanical Responses of Arabidopsis Thylakoid Membranes during PSII-Specific Illumination

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