Low-THz Vibrations of Biological Membranes

Abstract

A growing body of work has linked key biological activities to the mechanical properties of cellular membranes, and as a means of identification. Here, we present a computational approach to simulate and compare the vibrational spectra in the low- THz region for mammalian and bacterial membranes, investigating the effect of membrane asymmetry and composition, as well as the conserved frequencies of a specific cell. We find that asymmetry does not impact the vibrational spectra, and the impact of sterols depends on the mobility of the components of the membrane. We demonstrate that vibrational spectra can be used to distinguish between membranes and, therefore, could be used in identification of different organisms. The method presented, here, can be immediately extended to other biological structures (e.g., amyloid fibers, polysaccharides, and protein-ligand structures) in order to fingerprint and understand vibrations of numerous biologically-relevant nanoscale structures.

Molecular Architecture and Helicity of Bacterial Amyloid Nanofibers: Implications for the Design of Nanoscale Antibiotics

“…The results of this work provide insights on the properties and characteristics of PSM-derived amyloids and can aid in the design of antiamyloid compounds with nanoscale dimensions, exemplified by chiral nanoparticles . MD simulations can be used as a tool to assist in exploratory research aimed at unraveling the cross-binding of fibers, inhibiting or reversing protein aggregation, and understanding processes related to the vibrations of biological structures . Similarly, MD simulations may be an important tool when it comes to optimizing prospective nanomedicine candidates in the future .…”

“…44 MD simulations can be used as a tool to assist in exploratory research aimed at unraveling the cross-binding of fibers, inhibiting or reversing protein aggregation, and understanding processes related to the vibrations of biological structures. 50 Similarly, MD simulations may be an important tool when it comes to optimizing prospective nanomedicine candidates in the future. 44 The relationship between the nano/micro structure of the fibrils and their individual building blocks is also essential for the understanding and engineering of complex nanofiber-based materials structurally symilar to amyloid networks.…”

“…We find compelling evidence that a cross-β-sheet two-protofilament (2beta) structure is the most plausible structural model for PSMα1 nanofibers in solution that matches the experimental values of chirality, diameter, and helical periodicity (pitch) of mature PSMα1 nanofibers in solution. The 2β PSMα1 amyloid nanofiber model can be used to study nanofiber–antimicrobial interactions to elucidate a mechanism for biofilm manipulation using man-made antiamyloid biomimetic nanostructures, as well as to explore the propagation of vibrations across functional amyloids anchored to bacterial membranes. ,,, In addition to machine learning techniques recently developed by our team, , this study provides a structural understanding of amyloid fibers that can inform a set of MD-based design principles and can usher in an era of tailor-made NPs as nanobiotics as high-efficacy antibacterial agents.…”

“…The 2β PSMα1 amyloid nanofiber model can be used to study nanofiber−antimicrobial interactions to elucidate a mechanism for biofilm manipulation using man-made antiamyloid biomimetic nanostructures, as well as to explore the propagation of vibrations across functional amyloids anchored to bacterial membranes. 44,45,50,51 In addition to machine learning techniques recently developed by our team, 46,53 this study provides a structural understanding of amyloid fibers that can inform a set of MD-based design principles and can usher in an era of tailor-made NPs as nanobiotics as high-efficacy antibacterial agents.…”

Real Space and Time Imaging of Collective Headgroup Dipole Motions in Zwitterionic Lipid Bilayers

“…The study of collective molecular motions in hydrated phospholipid bilayers is a challenging area of science [1][2][3]. Although almost all liquid crystalline lipid bilayers undergo large molecular displacements, their intermolecular interactions are lipid specific [4][5][6][7].…”