Zachary A Levine

Zachary A Levine
Yale University | YU · Department of Molecular Biophysics and Biochemistry

PhD Physics

About

62
Publications
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1,222
Citations

Publications

Publications (62)
Article
Full-text available
The neuronal membrane-associated periodic spectrin skeleton (MPS) contributes to neuronal development, remodeling, and organization. Post-translational modifications impinge on spectrin, the major component of the MPS, but their role remains poorly understood. One modification targeting spectrin is cleavage by calpains, a family of calcium-activate...
Preprint
Full-text available
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways when they are solved by x-ray crystallography versus solution-based NMR spectroscopy. Given these discrepancies,...
Article
Obverse Cover: The cover image is based on the Original Article Analyses of protein cores reveal fundamental differences between solution and crystal structures by Corey O'Hern et al., https://doi.org/10.1002/prot.25884
Article
The ability to consistently distinguish real protein structures from computationally‐generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of pro...
Article
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structure...
Preprint
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of pro...
Article
Mitochondrially-derived peptides (MDPs) such as humanin (HN) have shown a remarkable ability to modulate neurological amyloids and apoptosis-associated proteins in cells and animal models. Recently, we found that humanin-like peptides also inhibit amyloid formation outside of neural environments in islet amyloid polypeptide (IAPP) fibrils and plaqu...
Preprint
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structure...
Article
We present the structure of an engineered protein‐protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr) residues. This Thr zipper structure suggests that the protein interface is stabilized by close‐packing of the Thr residues, with only one inter‐monomer hydrogen bond (H‐bond) between two of...
Chapter
Intrinsically disordered proteins (IDPs) and regions (IDRs) make up a significant part of the proteome and facilitate a wide range of physiological and pathological functions that are only beginning to be understood. As such, they are highly attractive targets for drug development and bioengineering. However, their inability to adopt well-defined s...
Chapter
Full-text available
Cells are the structural and functional unit of all living organisms and exhibit fundamental properties of life. Cells are surrounded by the cell membrane and subdivided into various compartments. Pulsed electric fields (PEFs) exert profound effects on cells by interacting with the cell membrane and other cellular components. This chapter describes...
Chapter
Membrane electropermeabilization describes the electric field-mediated depolarization, and subsequent breakdown of cellular membranes, and is widely used in clinical and academic environments to deliver extracellular materials into the cell interior. Recently, these methods have contributed to the optimization of food sterilization and next-generat...
Chapter
Atomistic simulations such as molecular dynamics (MD) simulations have revealed much about the fundamental biophysics of electroporation in homogeneous phospholipid bilayers; however, the structures and behaviors of live cellular membranes differ considerably from idealized zwitterionic lipid bilayers. Biological membranes contain both neutral and...
Article
Full-text available
Marine mussels use catechol-rich interfacial mussel foot proteins (mfps) as primers that attach to mineral surfaces via hydrogen, metal coordination, electrostatic, ionic, or hydrophobic bonds, creating a secondary surface that promotes bonding to the bulk mfps. Inspired by this biological adhesive primer, it is shown that a ≈1 nm thick catecholic...
Article
Intrinsically disordered proteins (IDPs) and protein regions can facilitate a wide variety of complex physiological processes such as binding, signaling, and formation of membraneless organelles. They can however also play pathological roles by aggregating into cytotoxic oligomers and fibrils. Characterizing the structure and function of disordered...
Article
Full-text available
The detailed molecular mechanisms underlying the permeabilization of cell membranes by pulsed electric fields (electroporation) remain obscure despite decades of investigative effort. To advance beyond descriptive schematics to the development of robust, predictive models, empirical parameters in existing models must be replaced with physics- and b...
Article
Despite the need for molecularly smooth self-assembled monolayers (SAMs) on silicon dioxide surfaces (the most common dielectric surface), current techniques are limited to non-ideal silane grafting. Here, we show unique bio-inspired zwitterionic molecules forming a molecularly smooth and uniformly thin SAM in “water” in <1 min on various dielectri...
Article
Full-text available
Translating sticky biological molecules-such as mussel foot proteins (MFPs)-into synthetic, cost-effective underwater adhesives with adjustable nano- and macroscale characteristics requires an intimate understanding of the glue's molecular interactions. To help facilitate the next generation of aqueous adhesives, we performed a combination of surfa...
Article
Using a combination of molecular dynamics simulations and experiments, we have examined the interactions of alkanes and phospholipids at charged interfaces in order to understand how interfacial charge densities affect the association of these two representative molecules with electrodes. Consistent with theory and experiment, these model systems r...
Article
Unregulated growth of amyloid plaques is associated with a large number of human degenerative diseases such as Alzheimer's Disease or Type II Diabetes, where the pathological misfolding and subsequent accumulation of amyloid plaques inhibits the proper functioning of nearby cells. Simulations and experiments have revealed that amyloid aggregates ar...
Article
The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dy...
Chapter
Membrane electropermeabilization describes the electric field-mediated depolarization, and subsequent breakdown of cellular membranes, and is widely used in clinical and academic environments to deliver extracellular materials into the cell interior. Recently, these methods have contributed to the optimization of food sterilization and next-generat...
Chapter
Atomistic simulations such as molecular dynamics (MD) simulations have revealed much about the fundamental biophysics of electroporation in homogeneous phospholipid bilayers; however, the structures and behaviors of live cellular membranes differ considerably from idealized zwitterionic lipid bilayers. Biological membranes contain both neutral and...
Article
Proteins-surface interactions are ubiquitous in both the cellular setting and in modern bio-engineering devices, but how such interactions impact protein stability is not well understood. We investigate the folding of the GB1 hairpin peptide in the presence of self-assembled monolayers and graphite like surfaces using replica exchange molecular dyn...
Article
Trp-cage is an artificial miniprotein that is one of the smallest and most stable self-folding proteins in aqueous environments, due to concerted hydrophobic shielding of a Trp residue by polyproline helices. Simulations have extensively characterized Trp-cage folding and denaturation, however the interactions of Trp-cage with organic surfaces (e.g...
Article
Full-text available
Non-thermal probing and stimulation with subnanosecond electric pulses and terahertz electromagnetic radiation may lead to new, minimally invasive diagnostic and therapeutic procedures and to methods for remote monitoring and analysis of biological systems, including plants, animals, and humans. To effectively engineer these still-emerging tools, w...
Article
Full-text available
Intrinsically disordered proteins (IDPs) are a unique class of proteins that have no stable native structure, a feature that allows them to adopt a wide variety of extended and compact conformations that facilitate a large number of vital physiological functions. One of the most well-known IDPs is the microtubule-associated tau protein, which regul...
Article
Full-text available
The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previo...
Conference Paper
Pulsed electric fields of nanosecond duration and high intensity (in the megavolt-per-meter range) have the ability to trigger functional modifications in biological cells, without irreversible disruption of the cell membranes. Although the biophysical mechanisms underlying the induced biological effects are not yet clear, promising applications ha...
Chapter
Pulsed electric fields of nanosecond duration and high intensity (in the megavolt-per-meter range) have the ability to trigger functional modifications in biological cells, without irreversible disruption of the cell membranes. Although the biophysical mechanisms underlying the induced biological effects are not yet clear, promising applications ha...
Article
Molecular dynamics (MD) simulations of electrophoretic transport of monovalent ions through field-stabilized electropores in POPC lipid bilayers permit systematic characterization of the conductive properties of lipid nanopores. The radius of the electropore can be controlled by the magnitude of the applied sustaining external electric field, which...
Article
Nanosecond, megavolt-per-meter electric pulses applied to biological cells can target subcellular structures with minimal loss of plasma membrane integrity, opening up new perspectives for intracellular manipulations. Experimentally observed effects of intense nanopulses include intracellular calcium release, externalization of phosphatidylserine (...
Article
Formation of a water bridge across the lipid bilayer is the first stage of pore formation in molecular dynamic (MD) simulations of electroporation, suggesting that the intrusion of individual water molecules into the membrane interior is the initiation event in a sequence that leads to the formation of a conductive membrane pore. To delineate more...
Article
Pulsed electric fields are used to permeabilize cell membranes in biotechnology and the clinic. Although molecular and continuum models provide compelling representations of the mechanisms underlying this phenomenon, a clear structural link between the biomolecular transformations displayed in molecular dynamics (MD) simulations and the micro- and...
Article
Full-text available
Electroporation is the formation of permeabilizing structures in the cell membrane under the influence of an externally imposed electric field. The resulting increased permeability of the membrane enables a wide range of biological applications, including the delivery of normally excluded substances into cells. While electroporation is used extensi...
Data
List of the performed simulations and the associated parameters. (XLSX)
Data
Computing energetic interactions of planar and vertical configurations of seven dipoles. (DOCX)
Data
Details of the protrusion waters–lipids interaction energy calculations. (DOCX)
Data
Choosing initial water-vacuum-water (WVW) configuration. (DOCX)
Data
Computing interaction energies for WVW and WLW configurations. (DOCX)
Article
Pulsed electric field permeabilization of living cell membranes forms the basis for widely used biotechnology protocols and an increasing number of therapeutic applications. Experimental observations of artificial membranes and whole cells and molecular and analytical models provide evidence that a membrane-spanning, hydrophilic, conductive pore ca...
Article
Monovalent ion concentration gradients, regulated by ion pumps and leak channels, are critical components of many cellular functions. This dynamic balance is disturbed by the electroporative permeabilization of the cell membrane, which bypasses the normal membrane barriers to transmembrane ion flux. A better understanding of ion transport during an...
Article
Molecular dynamics simulations of electroporation of homogeneous phospholipid bilayers show that the pore creation time is strongly dependent on the magnitude of the applied electric field. Here, we investigated whether heterogeneous bilayers containing phospholipids with zwitterionic and anionic headgroups exhibit a similar dependence. To facilita...
Article
Experimental studies have shown that cell membranes can be permeabilized by exposure to nanosecond and subnanosecond electric pulses with megavolt-per-meter amplitudes [1,2]. For pulses in the low nanosecond and subnanosecond range, the rise time of the actual waveform delivered to a biological load is a significant percentage of the entire pulse d...
Article
A recent study showed that water forms cone-like structures at a vacuum or air interface under a sufficiently high electric field [1]. This protruding water formation may be a key step in the initiation of electroporation of lipid bilayers and cell membranes. In molecular dynamics (MD) simulations of water-vacuum-water (WVW) systems, we observe the...
Article
Negative electrophoretic mobilities of oil in water are widely interpreted in terms of adsorption of hydroxide leading to negative surface charge. Challenging this traditional view, an increasing body of evidence suggests surface depletion of hydroxide and surface accumulation of hydronium leading to a positive surface charge. We present results fr...
Article
Electropermeabilization, an electric field-induced modification of the barrier functions of the cell membrane, is widely used in laboratories and increasingly in the clinic; but the mechanisms and physical structures associated with the electromanipulation of membrane permeability have not been definitively characterized. Indirect experimental obse...
Article
Understanding the behavior of water in atomic-scale detail is essential to explaining the microscopic dynamics of such phenomena as electroporation, electrospinning, electrospraying, and electric-field-driven evaporation. In this study we employ molecular dynamics simulations to investigate water-vacuum systems under the influence of an externally...
Article
To aid in understanding the mechanism of electric field-driven pore formation in lipid bilayers, we propose a scheme for characterizing the life cycle of a transient membrane electropore, from the formation of the initial defect to the restoration of the intact bilayer. We apply this analysis to heterogeneous phospholipid bilayers (phosphatidylchol...
Article
Full-text available
Reversible electropermeabilization (electroporation) is widely used to facilitate the introduction of genetic material and pharmaceutical agents into living cells. Although considerable knowledge has been gained from the study of real and simulated model membranes in electric fields, efforts to optimize electroporation protocols are limited by a la...
Article
Molecular dynamics (MD) studies showing that oxidized lipids increase the frequency of water defects in phospholipid bilayers suggest that the presence of oxidized lipids in a bilayer will also increase the sensitivity of the bilayer to electropermeabilization. To investigate this possibility we applied external electric fields during MD simulation...

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