Ram Avinery | Tel Aviv University (original) (raw)

Papers by Ram Avinery

Nano letters, Jan 30, 2015

The structural plasticity of intrinsically disordered proteins serves as a rich area for scientif... more The structural plasticity of intrinsically disordered proteins serves as a rich area for scientific inquiry. Such proteins lack a fix 3D structure but can interact with multiple partners through numerous weak bonds. Nevertheless, this intrinsic plasticity possesses a challenging hurdle in their characterization. We underpin the intermolecular interactions between intrinsically disordered neurofilaments, in various hydrated conditions, using grafted gold nanoparticle (NP) tags. Beyond its biological significance, this approach can be applied to modify the surface interaction of NPs for the creation of future tunable "smart" hybrid biomaterials.

Nano letters, Jan 30, 2015

The structural plasticity of intrinsically disordered proteins serves as a rich area for scientif... more The structural plasticity of intrinsically disordered proteins serves as a rich area for scientific inquiry. Such proteins lack a fix 3D structure but can interact with multiple partners through numerous weak bonds. Nevertheless, this intrinsic plasticity possesses a challenging hurdle in their characterization. We underpin the intermolecular interactions between intrinsically disordered neurofilaments, in various hydrated conditions, using grafted gold nanoparticle (NP) tags. Beyond its biological significance, this approach can be applied to modify the surface interaction of NPs for the creation of future tunable "smart" hybrid biomaterials.

Biophysical Journal, Jun 4, 2013

Voltage-dependent calcium channels (CaV) enable the inward flow of calcium currents for a wide ra... more Voltage-dependent calcium channels (CaV) enable the inward flow of calcium currents for a wide range of cells. CaV1 and CaV2 subtype α1 subunits form the conducting pore using four repeated membrane domains connected by intracellular linkers. The domain I-II linker connects to the membrane gate (IS6), forming an α-helix, and is bound to the CaVβ subunit. Previous studies indicated that this region may or may not form a continuous helix depending on the CaV subtype, thereby modulating channel activation and inactivation properties. Here, we used small-angle x-ray scattering and ensemble modeling analysis to investigate the solution structure of these linkers, extending from the membrane domain and including the CaVβ-binding site, called the proximal linker (PL). The results demonstrate that the CaV1.2 PL is more flexible than the CaV2.2 PL, the flexibility is intrinsic and not dependent on CaVβ binding, and the flexibility can be most easily explained by the presence of conserved glycines. Our analysis also provides a robust example of investigating protein domains in which flexibility plays an essential role.

Current opinion in biotechnology, 2013

X-ray scattering is one of the most prominent structural characterization techniques in biology. ... more X-ray scattering is one of the most prominent structural characterization techniques in biology. The key advantage of X-ray scattering is its ability to penetrate and weakly interact with the bare studied materials. In addition, X-ray scattering does not require any tags, markers or modification to the sample under examination, and is not limited by the nature of the surrounding environment. The main handicapping limitation of X-ray scattering is the subject of particles polydispersity. However, the monodispersity in biological complexes and supra-molecular interactions makes them ideal for structural and interaction studies in particular when combined with higher (e.g. NMR) and/or lower resolution (e.g. optical microscopy) techniques. This review seeks to highlight some of the major recent achievements in the field of X-ray scattering as being implemented for complex biological systems.

Genetic …, 2010

An important component in the analysis of genome-wide association studies involves the imputation... more An important component in the analysis of genome-wide association studies involves the imputation of genotypes that have not been measured directly in the studied samples. The imputation procedure uses the linkage disequilibrium (LD) structure in the population to infer the genotype of an unobserved single nucleotide polymorphism. The LD structure is normally learned from a dense genotype map of a reference population that matches the studied population. In many instances there is no reference population that exactly matches the studied population, and a natural question arises as to how to choose the reference population for the imputation. Here we present a Coalescent-based method that addresses this issue. In contrast to the current paradigm of imputation methods, our method assigns a different reference dataset for each sample in the studied population, and for each region in the genome. This allows the flexibility to account for the diversity within populations, as well as across populations. Furthermore, because our approach treats each region in the genome separately, our method is suitable for the imputation of recently admixed populations. We evaluated our method across a large set of populations and found that our choice of reference data set considerably improves the accuracy of imputation, especially for regions with low LD and for populations without a reference population available as well as for admixed populations such as the Hispanic population. Our method is generic and can potentially be incorporated in any of the available imputation methods as an add-on.

Nano letters, Jan 30, 2015

The structural plasticity of intrinsically disordered proteins serves as a rich area for scientif... more The structural plasticity of intrinsically disordered proteins serves as a rich area for scientific inquiry. Such proteins lack a fix 3D structure but can interact with multiple partners through numerous weak bonds. Nevertheless, this intrinsic plasticity possesses a challenging hurdle in their characterization. We underpin the intermolecular interactions between intrinsically disordered neurofilaments, in various hydrated conditions, using grafted gold nanoparticle (NP) tags. Beyond its biological significance, this approach can be applied to modify the surface interaction of NPs for the creation of future tunable "smart" hybrid biomaterials.

Nano letters, Jan 30, 2015

The structural plasticity of intrinsically disordered proteins serves as a rich area for scientif... more The structural plasticity of intrinsically disordered proteins serves as a rich area for scientific inquiry. Such proteins lack a fix 3D structure but can interact with multiple partners through numerous weak bonds. Nevertheless, this intrinsic plasticity possesses a challenging hurdle in their characterization. We underpin the intermolecular interactions between intrinsically disordered neurofilaments, in various hydrated conditions, using grafted gold nanoparticle (NP) tags. Beyond its biological significance, this approach can be applied to modify the surface interaction of NPs for the creation of future tunable "smart" hybrid biomaterials.

Biophysical Journal, Jun 4, 2013

Voltage-dependent calcium channels (CaV) enable the inward flow of calcium currents for a wide ra... more Voltage-dependent calcium channels (CaV) enable the inward flow of calcium currents for a wide range of cells. CaV1 and CaV2 subtype α1 subunits form the conducting pore using four repeated membrane domains connected by intracellular linkers. The domain I-II linker connects to the membrane gate (IS6), forming an α-helix, and is bound to the CaVβ subunit. Previous studies indicated that this region may or may not form a continuous helix depending on the CaV subtype, thereby modulating channel activation and inactivation properties. Here, we used small-angle x-ray scattering and ensemble modeling analysis to investigate the solution structure of these linkers, extending from the membrane domain and including the CaVβ-binding site, called the proximal linker (PL). The results demonstrate that the CaV1.2 PL is more flexible than the CaV2.2 PL, the flexibility is intrinsic and not dependent on CaVβ binding, and the flexibility can be most easily explained by the presence of conserved glycines. Our analysis also provides a robust example of investigating protein domains in which flexibility plays an essential role.

Current opinion in biotechnology, 2013

X-ray scattering is one of the most prominent structural characterization techniques in biology. ... more X-ray scattering is one of the most prominent structural characterization techniques in biology. The key advantage of X-ray scattering is its ability to penetrate and weakly interact with the bare studied materials. In addition, X-ray scattering does not require any tags, markers or modification to the sample under examination, and is not limited by the nature of the surrounding environment. The main handicapping limitation of X-ray scattering is the subject of particles polydispersity. However, the monodispersity in biological complexes and supra-molecular interactions makes them ideal for structural and interaction studies in particular when combined with higher (e.g. NMR) and/or lower resolution (e.g. optical microscopy) techniques. This review seeks to highlight some of the major recent achievements in the field of X-ray scattering as being implemented for complex biological systems.

Genetic …, 2010

An important component in the analysis of genome-wide association studies involves the imputation... more An important component in the analysis of genome-wide association studies involves the imputation of genotypes that have not been measured directly in the studied samples. The imputation procedure uses the linkage disequilibrium (LD) structure in the population to infer the genotype of an unobserved single nucleotide polymorphism. The LD structure is normally learned from a dense genotype map of a reference population that matches the studied population. In many instances there is no reference population that exactly matches the studied population, and a natural question arises as to how to choose the reference population for the imputation. Here we present a Coalescent-based method that addresses this issue. In contrast to the current paradigm of imputation methods, our method assigns a different reference dataset for each sample in the studied population, and for each region in the genome. This allows the flexibility to account for the diversity within populations, as well as across populations. Furthermore, because our approach treats each region in the genome separately, our method is suitable for the imputation of recently admixed populations. We evaluated our method across a large set of populations and found that our choice of reference data set considerably improves the accuracy of imputation, especially for regions with low LD and for populations without a reference population available as well as for admixed populations such as the Hispanic population. Our method is generic and can potentially be incorporated in any of the available imputation methods as an add-on.