Publications

2022
Shemesh A, Ginsburg A, Dharan R, Levi-Kalisman Y, Ringel I, Raviv U. Mechanism of Tubulin Oligomers and Single-Ring Disassembly Catastrophe. The Journal of Physical Chemistry Letters [Internet]. 2022;13 (23) :5246-5252. Publisher's Version
Shemesh A, Ginsburg A, Dharan R, Kalisman-Levi Y, Ringel I, Raviv U. Mechanism of Tubulin Oligomers and Single-Rings Disassembly Catastrophe. ChemRxiv [Internet]. 2022. Publisher's Version
Asor R, Singaram SW, Levi-Kalisman Y, Hagan MF, Raviv U. Effect of Ionic Strength on the Assembly of Simian Vacuolating Virus Capsid Protein Around Poly(Styrene Sulfonate). bioRxiv [Internet]. 2022. Publisher's VersionAbstract

{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. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with combinatorial intermediates, and therefore the mechanism of the reaction is poorly understood. In this paper, we determined the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by solution small-angle X-ray scattering (SAXS) and cryo-TEM. To analyze the data, we performed Brownian dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures that were consistent with the experimental data. We found that close to physiological ionic strength

2021
Sadeh AS, Dharan R, Ghareeb H, Metanis N, Ringel I, Raviv U. Effect of Tubulin Self-Association on GTP Hydrolysis and Nucleotide Exchange Reactions. ChemRxiv [Internet]. 2021. Publisher's Version
Shemesh A, Ginsburg A, Dharan R, Levi-Kalisman Y, Ringel I, Raviv U. Structure and Energetics of GTP- and GDP-Tubulin Isodesmic Self-Association. ACS Chemical Biology [Internet]. 2021;16 (11) :2212–2227. Publisher's Version
Dharan R, Shemesh A, Millgram A, Zalk R, Frank GA, Levi-Kalisman Y, Ringel I, Raviv U. Hierarchical Assembly Pathways of Spermine-Induced Tubulin Conical-Spiral Architectures. ACS Nano [Internet]. 2021;15 (5) :8836–8847. Publisher's Version
Schilt Y, Berman T, Wei X, Nativ-Roth E, Barenholz Y, Raviv U. Effect of the ammonium salt anion on the structure of doxorubicin complex and PEGylated liposomal doxorubicin nanodrugs. Biochimica et Biophysica Acta (BBA) - General Subjects [Internet]. 2021;1865 (5) :129849. Publisher's VersionAbstract

Background In Doxil®, PEGylated nanoliposomes are created by hydration of the lipids in ammonium sulfate, and are remotely loaded with doxorubicin by a transmembrane ammonium gradient. The ammonium sulfate is then removed from the external aqueous phase, surrounding the liposomes, and replaced by an isoosmotic sucrose solution in 10 mM histidine buffer at pH 6.5. Methods We prepared PEGylated liposomal doxorubicin (PLD) with a series of ammonium monovalent salts that after remote loading became the intraliposome doxorubicin counteranions. We analyzed the liposomes by solution X-ray scattering, differential scanning calorimetry, and electron micropscopy. Results PLDs prepared with sulfonic acid derivatives as counteranion exhibited chemical and physical stabilities. We determined the effect of these ammonium salt counteranions on the structure, morphology, and thermotropic behavior of the PEGylated nanoliposomes, formed before and after doxorubicin loading, and the bulk properties of the doxorubicin-counteranion complexes. By comparing the structure of the doxorubicin complexes in the bulk and inside the nanoliposomes, we revealed the effect of confinement on the structure and doxorubicin release rate for each of the derivatives of the ammonium sulfonic acid counteranions. Conclusions We found that the extent and direction of the doxorubicin confinement effect and its release rate were strongly dependent on the type of counteranion. The counteranions, however, neither affected the structure and thermotropic behavior of the liposome membrane, nor the thickness and density of the liposome PEG layers. In an additional study, it was demonstrated that PLD made with ammonium-methane sulfonate exhibit a much lower Hand and Foot syndrome. General significance The structure, physical state, and pharmacokinetics of doxorubicin in PEGylated nanoliposomes, prepared by transmembrane remote loading using gradients of ammonium salts, strongly depend on the counteranions.

2020
Fink L, Allolio C, Feitelson J, Tamburu C, Harries D, Raviv U. Bridges of Calcium Bicarbonate Tightly Couple Dipolar Lipid Membranes. Langmuir [Internet]. 2020;36 (36) :10715–10724. Publisher's Version
Shukrun Farrell E, Schilt Y, Moshkovitz MY, Levi-Kalisman Y, Raviv U, Magdassi S. 3D Printing of ordered mesoporous silica complex structures. Nano Letters [Internet]. 2020;20 (9) :6598–6605. Publisher's Version
Waltmann C, Asor R, Raviv U, Olvera de la Cruz M. Assembly and Stability of Simian Virus 40 Polymorphs. ACS Nano [Internet]. 2020;14 (4) :4430-4443. Publisher's Version
Asor R, Schlicksup CJ, Zhao Z, Zlotnick A, Raviv U. Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly. Journal of the American Chemical Society [Internet]. 2020; 142 (17) :7868–7882. Publisher's Version
Asor R, Khaykelson D, Ben-nun-Shaul O, Levi-Kalisman Y, Oppenheim A, Raviv U. pH Stability and Disassembly Mechanism of Wild-Type Simian Virus 40. Soft Matter [Internet]. 2020;16 (11) :2803-2814. Publisher's VersionAbstract

Virus are remarkable self-assembled nanobiomaterial-based machines, exposed to a wide range of pH values. Extreme pH values can induce dramatic structural changes, critical for the function of the virus nanoparticles including assembly and genome uncoating. Tuning cargo - capsid interactions is essential for designing viral-based delivery systems. Here we show how pH controls the structure and activity of wild-type simian virus 40 (wtSV40) and the interplay between its cargo and capsid. Using cryo-TEM and solution X-ray scattering, we found that wtSV40 was stable between pH 5.5 and 9, and only slightly swelled with increasing pH. At pH 3, the particles aggregated, while capsid protein pentamers continued to coat the virus cargo but lost their positional correlations. Infectivity was only partly lost after the particles had been returned to pH 7. At pH 10 or higher, the particles were unstable, lost their infectivity, and disassembled. Using time-resolved experiments we discovered that disassembly began by swelling of the particles, poking a hole in the capsid through which the genetic cargo escaped, and followed by a slight shrinking of the capsids and complete disassembly. These findings provide insight into the fundamental intermolecular forces, essential for SV40 function, and for designing virus-based nanobiomaterials, including delivery systems and antiviral drugs.

Khaykelson D, Raviv U. Studying viruses using solution X-ray scattering. Biophysical Reviews [Internet]. 2020;12 :41–48. Publisher's VersionAbstract

Viruses have been of interest to mankind since their discovery as small infectious agents in the nineteenth century. Because many viruses cause diseases to humans and agriculture, they were rigorously studied for biological and medical purposes. Viruses have remarkable properties such as the symmetry and self-assembly of their protein envelope, maturation into infectious virions, structural stability, and disassembly. Solution X-ray scattering can probe structures and reactions in solutions, down to subnanometer spatial resolution and millisecond temporal resolution. It probes the bulk solution and reveals the average shape and average mass of particles in solution and can be used to study kinetics and thermodynamics of viruses at different stages of their life cycle. Here we review recent work that demonstrates the capabilities of solution X-ray scattering to study in vitro the viral life cycle.

2019
Dharan R, Shemesh A, Millgram A, Levi-Kalisman Y, Ringel I, Raviv U. Hierarchical Assembly Pathways of Spermine Induced Tubulin Conical-Spiral Architectures. [Internet]. 2019. Publisher's Version
Shaltiel L, Shemesh A, Raviv U, Barenholz Y, Levi-Kalisman Y. Synthesis and Characterization of Thiolate-Protected Gold Nanoparticles of Controlled Diameter. J. Phys. Chem. C [Internet]. 2019;123 (46) :28486-28493. Publisher's Version
Safinya CR, Chung PJ, Song C, Li Y, Miller HP, Choi MC, Raviv U, Ewert KK, Wilson L, Feinstein SC. Minireview-Microtubule and Tubulin Oligomers: Shape Transitions and Assembly by Intrinsically Disordered Protein Tau and Cationic Biomolecules. Langmuir [Internet]. 2019;35 (48) :15970–15978. Publisher's Version
Fink L, Steiner A, Szekely O, Szekely P, Raviv U. Structure and Interactions between Charged Lipid Membranes in the Presence of Multivalent Ions. Langmuir [Internet]. 2019;35 (30) :9694-9703. Publisher's Version
Asor R, Selzer L, Schlicksup CJ, Zhao Z, Zlotnick A, Raviv U. Assembly Reactions of Hepatitis B Capsid Protein into Capsid Nanoparticles Follow a Narrow Path Through a Complex Reaction Landscape. ACS Nano [Internet]. 2019;13 (7) :7610-7626. Publisher's Version
Zhao Z, Che-Yen Wang J, Gonzalez-Gutierrez G, Venkatakrishnan B, Asor R, Khaykelson D, Raviv U, Zlotnick A. Structural differences between the Woodchuck hepatitis virus core protein in dimer and capsid states are consistent with entropic and conformational regulation of assembly. Journal of Virology [Internet]. 2019 :JVI.00141-19. Publisher's Version
Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Fink L, Tekoah R, Levartovsky Y, Khaykelson D, Dharan R, Fellig A, et al. D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. Journal of Applied Crystallography [Internet]. 2019;52 (1) :219-242. Publisher's Version

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