Explanipedia

Effects of Chemical Cross-Linking on the Structure of Proteins and Protein Assemblies Open

Tamar Tayri-Wilk, Nir Kalisman, Uri Raviv · 2025

Chemical cross-linking is frequently used in structural biology for protein stabilization and probing protein structures, often in combination with mass spectrometry (XL-MS). These applications assume that chemical cross-linking does not s…

Modulating the Curvature of Protein Self-Assembled Spiral Nanotubules Open

Ariel Cohen, Itai Ben-Nun, Raviv Dharan, Tamar Tayri-Wilk, Asaf Shemesh , et al. · 2025

Structural transformations from ribbons to twisted ribbons to helical ribbons are often observed across supramolecular assemblies and macroscopic structures and can be described under a consistent theoretical framework. Conical molecular s…

E+: Software for Hierarchical Modeling of Electron Scattering from Complex Structures Open

Eytan Balken, Daniel Khaykelson, Itai Ben-Nun, Yael Levi‐Kalisman, Lothar Houben , et al. · 2025

In modern nanobeam transmission electron microscopy methods, such as 4D-STEM, a converged electron nanobeam is scanned across a sample. Its 2D scattering pattern is recorded at each sample position, mapping the local sample structure. One …

Anisotropic membrane with high proton conductivity sustaining upon dehydration Open

J. Li, Jay Prakash Singh, Vadim Neklyudov, Mikhail Stolov, Ziyi Yuan , et al. · 2024

In fuel cells and electrolyzers, suboptimal proton conductivity and its dramatic drop at low humidity remain major drawbacks in proton exchange membranes (PEMs), including current benchmark Nafion. Sustained through-plane (TP) alignment of…

Sound-mediated nucleation and growth of amyloid fibrils Open

Anna Kozell, Alexey V. Solomonov, Roman Gaidarov, Doron Benyamin, Irit Rosenhek‐Goldian , et al. · 2024

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, conseque…

Fine Structural Analysis of Degummed Fibroin Fibers Reveals Its Superior Mechanical Capabilities Open

Ulyana Shimanovich, Dror Eliaz, Israel Kellersztein, Marco Elvino Miali, Doron Benyamin , et al. · 2024

Bombyx mori silk fibroin fibers constitute a class of protein building blocks capable of functionalization and reprocessing into various material formats. The properties of these fibers are typically affected by the intense thermal treatme…

Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis Open

Daniel Khaykelson, Roi Asor, Zhongchao Zhao, Christopher J. Schlicksup, Adam Zlotnick , et al. · 2024

Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Afric…

Fine structural analysis of non-thermal degummed fibroin fibers reveals its superior mechanical capabilities Open

Dror Eliaz, Israel Kellersztein, Marco Elvino Miali, Doron Benyamin, Ori Brookstein , et al. · 2024

Bombyx mori silk fibroin fibers constitute a class of protein building blocks capable of func-tionalization and reprocessing into various material formats. The properties of these fibers are typically affected by the intense thermal treatm…

Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate) Open

Roi Asor, Surendra W. Singaram, Yael Levi‐Kalisman, Michael F. Hagan, Uri Raviv · 2023

Sound-mediated nucleation and growth of amyloid fibrils Open

Anna Kozell, Alexey V. Solomonov, Roman Gaidarov, Doron Benyamin, Irit Rosenhek‐Goldian , et al. · 2023

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, conseque…

Upgrade of <i>D</i>+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations Open

Eytan Balken, Itai Ben-Nun, Amos Fellig, Daniel Khaykelson, Uri Raviv · 2023

This article presents an upgrade of the D + software [Ginsburg et al. (2019). J. Appl. Cryst. 52 , 219–242], expanding its hierarchical solution X-ray scattering modeling capabilities for fiber diffraction and single crystallographic orien…

Modulating amyloids’ formation path with sound energy Open

Anna Kozell, Dror Eliaz, Alexey V. Solomonov, Doron Benyamin, Guy Shmul , et al. · 2023

Protein folding is crucial for biological activity. Proteins’ failure to fold correctly underlies various pathological processes, including amyloidosis, the aggregation of insoluble proteins (e.g., lysozymes) in organs. The exact condition…

Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers Open

Dror Eliaz, Suman Paul, Doron Benyamin, Adrian Cernescu, Sidney Cohen , et al. · 2022

Mechanism of Tubulin Oligomers and Single-Ring Disassembly Catastrophe Open

Asaf Shemesh, Avi Ginsburg, Raviv Dharan, Yael Levi‐Kalisman, Israel Ringel , et al. · 2022

Cold tubulin dimers coexist with tubulin oligomers and single rings. These structures are involved in microtubule assembly; however, their dynamics are poorly understood. Using state-of-the-art solution synchrotron time-resolved small-angl…

Mechanism of Tubulin Oligomers and Single-Rings Disassembly Catastrophe Open

Asaf Shemesh, Avi Ginsburg, Raviv Dharan, Yael Levi‐Kalisman, Israel Ringel , et al. · 2022

Cold tubulin dimers coexist with tubulin oligomers and single-rings. These structures are involved in microtubule assembly, however, their dynamics are poorly understood. Using state-of-the-art solution synchrotron time-resolved small-angl…

Effect of Tubulin Self-Association on GTP Hydrolysis and Nucleotide Exchange Reactions Open

Asaf Sadeh, Raviv Dharan, Hiba Ghareeb, Norman Metanis, Israel Ringel , et al. · 2022

Tubulin nucleation, microtubule (MT) assembly, stability, and dynamics depend on GTP hydrolysis and nucleotide exchange reactions. We investigated how the self-association of isolated tubulin dimers affects the rate of GTP hydrolysis and t…

Effect of Ionic Strength on the Assembly of Simian Vacuolating Virus Capsid Protein Around Poly(Styrene Sulfonate) Open

Roi Asor, Surendra W. Singaram, Yael Levi‐Kalisman, Michael F. Hagan, Uri Raviv · 2022

Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent like RNA, DNA, or a charged polymer. Electros…

Dehydration does not affect lipid-based hydration lubrication Open

Yihui Dong, Nir Kampf, Yaelle Schilt, Wei Cao, Uri Raviv , et al. · 2022

Lipid-headgroup dehydration by DMSO, which should increase friction, is offset by both higher areal head-group density and by rigidity-enhancement of the lipid bilayers, both of which act to reduce frictional dissipation.

Effect of Tubulin Self-Association on GTP Hydrolysis and Nucleotide Exchange Reactions Open

Asaf Sadeh, Raviv Dharan, Hiba Ghareeb, Norman Metanis, Israel Ringel , et al. · 2021

Tubulin nucleation, microtubule assembly, stability, and dynamics depend on fluxes of chemical energy, controlled by hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP), and nucleotide exchange reactions. In this pape…

Effect of Tubulin Self-Association on GTP Hydrolysis and Nucleotide Exchange Reactions Open

Asaf Sadeh, Raviv Dharan, Hiba Ghareeb, Norman Metanis, Israel Ringel , et al. · 2021

Tubulin nucleation, microtubule assembly, stability, and dynamics depend on fluxes of chemical energy, controlled by hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP), and nucleotide exchange reactions. In this pape…

Bridges of Calcium Bicarbonate Tightly Couple Dipolar Lipid Membranes Open

Lea Fink, Christoph Allolio, Jehuda Feitelson, Carmen Tamburu, Daniel Harries , et al. · 2020

The interaction between lipid membranes and ions is associated with a range of key physiological processes. Most earlier studies have focused on the interaction of lipids with cations, while the specific effects of the anions have been lar…

3D Printing of Ordered Mesoporous Silica Complex Structures Open

Efrat Shukrun Farrell, Yaelle Schilt, May Yam Moshkovitz, Yael Levi‐Kalisman, Uri Raviv , et al. · 2020

Ordered mesoporous silica materials gain high interest because of their potential applications in catalysis, selective adsorption, separation, and controlled drug release. Due to their morphological characteristics, mainly the tunable, ord…

Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly Open

Roi Asor, Christopher J. Schlicksup, Zhongchao Zhao, Adam Zlotnick, Uri Raviv · 2020

There are ∼10³⁰ possible intermediates on the assembly path from hepatitis B capsid protein dimers to the 120-dimer capsid. If every intermediate was tested, assembly would often get stuck in an entropic trap and essentially eve…

Assembly and Stability of Simian Virus 40 Polymorphs Open

Curt Waltmann, Roi Asor, Uri Raviv, Mónica Olvera de la Cruz · 2020

Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate t…

Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly Open

Roi Asor, Christopher J. Schlicksup, Zhongchao Zhao, Adam Zlotnick, Uri Raviv · 2020

There are about 10³⁰ possible intermediates on the assembly path from hepatitis B capsid protein dimers to the 120-dimer capsid. If every intermediate was tested, assembly would often get stuck in an entropic trap and essentiall…

Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly Open

Roi Asor, Christopher J. Schlicksup, Zhongchao Zhao, Adam Zlotnick, Uri Raviv · 2020

There are about 10 30 possible intermediates on the assembly path from hepatitis B capsid protein dimers to the 120-dimer capsid. If every intermediate was tested, assembly would often get stuck in an entropic trap and essentially every ca…

Studying viruses using solution X-ray scattering Open

Daniel Khaykelson, Uri Raviv · 2020

Hierarchical Assembly Pathways of Spermine Induced Tubulin Conical-Spiral Architectures Open

Raviv Dharan, Asaf Shemesh, Abigail Millgram, Yael Levi‐Kalisman, Israel Ringel , et al. · 2020

Tubulin, an essential cytoskeletal protein, assembles into various morphologies by interacting with cellular factors. Spermine, an endogenous polyamine, promotes and stabilizes tubulin assemblies. Yet, the assembled structures and their fo…

pH stability and disassembly mechanism of wild-type simian virus 40 Open

Roi Asor, Daniel Khaykelson, Orly Ben-nun-Shaul, Yael Levi‐Kalisman, Ariella Oppenheim , et al. · 2020

At high pH, wtSV40 swells, and its minichromosome pokes a hole in the capsid and escapes, following which the capsid disintegrates.

Hierarchical Assembly Pathways of Spermine Induced Tubulin Conical-Spiral Architectures Open

Raviv Dharan, Asaf Shemesh, Abigail Millgram, Yael Levi‐Kalisman, Israel Ringel , et al. · 2019

Tubulin dimers are flexible entities serving as building blocks for construction of cellular polymers essential for the cytoskeleton. The conformational state of the dimer dictates the exact formation of assembly and can be regulated by ce…

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