Nanopore sensing: A physical-chemical approach

Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.     

Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography

Cyanobacteria, descendants of the endosymbiont that gave rise to modern-day chloroplasts, are vital contributors to global biological energy conversion processes. A thorough understanding of the physiology of cyanobacteria requires detailed knowledge of these organisms at the level of cellular architecture and organization. In these prokaryotes, the large membrane protein complexes of the photosynthetic and respiratory electron transport chains function in the intracellular thylakoid membranes. Like plants, the architecture of the thylakoid membranes in cyanobacteria has direct impact on cellular bioenergetics, protein transport, and molecular trafficking. However, whole-cell thylakoid organization in cyanobacteria is not well understood. Here we present, by using electron tomography, an in-depth analysis of the architecture of the thylakoid membranes in a unicellular cyanobacterium, Cyanothece sp. ATCC 51142. Based on the results of three-dimensional tomographic reconstructions of near-entire cells, we determined that the thylakoids in Cyanothece 51142 form a dense and complex network that extends throughout the entire cell. This thylakoid membrane network is formed from the branching and splitting of membranes and encloses a single lumenal space. The entire thylakoid network spirals as a peripheral ring of membranes around the cell, an organization that has not previously been described in a cyanobacterium. Within the thylakoid membrane network are areas of quasi-helical arrangement with similarities to the thylakoid membrane system in chloroplasts. This cyanobacterial thylakoid arrangement is an efficient means of packing a large volume of membranes in the cell while optimizing intracellular transport and trafficking.     

Biological effects of electromagnetic fields

Life on earth has evolved in a sea of natural electromagnetic (EM) fields. Over the past century, this natural environment has sharply changed with introduction of a vast and growing spectrum of man-made EM fields. From models based on equilibrium thermodynamics and thermal effects, these fields were initially considered too weak to interact with biomolecular systems, and thus incapable of influencing physiological functions. Laboratory studies have tested a spectrum of EM fields for bioeffects at cell and molecular levels, focusing on exposures at athermal levels. A clear emergent conclusion is that many observed interactions are not based on tissue heating. Modulation of cell surface chemical events by weak EM fields indicates a major amplification of initial weak triggers associated with binding of hormones, antibodies, and neurotransmitters to their specific binding sites. Calcium ions play a key role in this amplification. These studies support new concepts of communication between cells across the barriers of cell membranes; and point with increasing certainty to an essential physical organization in living matter, at a far finer level than the structural and functional image defined in the chemistry of molecules. New collaborations between physical and biological scientists define common goals, seeking solutions to the physical nature of matter through a strong focus on biological matter. The evidence indicates mediation by highly nonlinear, nonequilibrium processes at critical steps in signal coupling across cell membranes. There is increasing evidence that these events relate to quantum states and resonant responses in biomolecular systems, and not to equilibrium thermodynamics associated with thermal energy exchanges and tissue heating.     

Plasma Lithography Surface Patterning for Creation of Cell Networks

Systematic manipulation of a cell microenvironment with micro- and nanoscale resolution is often required for deciphering various cellular and molecular phenomena. To address this requirement, we have developed a plasma lithography technique to manipulate the cellular microenvironment by creating a patterned surface with feature sizes ranging from 100 nm to millimeters. The goal of this technique is to be able to study, in a controlled way, the behaviors of individual cells as well as groups of cells and their interactions.This plasma lithography method is based on selective modification of the surface chemistry on a substrate by means of shielding the contact of low-temperature plasma with a physical mold. This selective shielding leaves a chemical pattern which can guide cell attachment and movement. This pattern, or surface template, can then be used to create networks of cells whose structure can mimic that found in nature and produces a controllable environment for experimental investigations. The technique is well suited to studying biological phenomenon as it produces stable surface patterns on transparent polymeric substrates in a biocompatible manner. The surface patterns last for weeks to months and can thus guide interaction with cells for long time periods which facilitates the study of long-term cellular processes, such as differentiation and adaption. The modification to the surface is primarily chemical in nature and thus does not introduce topographical or physical interference for interpretation of results. It also does not involve any harsh or toxic substances to achieve patterning and is compatible for tissue culture. Furthermore, it can be applied to modify various types of polymeric substrates, which due to the ability to tune their properties are ideal for and are widely used in biological applications. The resolution achievable is also beneficial, as isolation of specific processes such as migration, adhesion, or binding allows for discrete, clear observations at the single to multicell level.This method has been employed to form diverse networks of different cell types for investigations involving migration, signaling, tissue formation, and the behavior and interactions of neurons arraigned in a network.     

Electric Field Orientation for Gene Delivery Using High-Voltage and Low-Voltage Pulses

Electropermeabilization is a biological physical process in response to the presence of an applied electric field that is used for the transfer of hydrophilic molecules such as anticancer drugs or DNA across the plasma membranes of living cells. The molecular processes that support the transfer are poorly known. The aim of our study was to investigate the effect of high-voltage and low-voltage (HVLV) pulses in vitro with different orientations on cell permeabilization, viability and gene transfection. We monitored the permeabilization with unipolar and bipolar HVLV pulses with different train repetition pulses, showing that HVLV pulses increase cell permeabilization and cell viability. Gene transfer was also observed by measuring green fluorescent protein (GFP) expression. The expression was the same for HVLV pulses and electrogenotherapy pulses for in vitro experimentation. As the viability was better preserved for HVLV-pulsed cells, we managed to increase the number of GFP-expressing cells by up to 65?% under this condition. The use of bipolar HVLV train pulses increased gene expression to a higher extent, probably by affecting a larger part of the cell surface.     

From mosaic to patchwork: matching lipids and proteins in membrane organization

Biological membranes encompass and compartmentalize cells and organelles and are a prerequisite to life as we know it. One defining feature of membranes is an astonishing diversity of building blocks. The mechanisms and principles organizing the thousands of proteins and lipids that make up membrane bilayers in cells are still under debate. Many terms and mechanisms have been introduced over the years to account for certain phenomena and aspects of membrane organization and function. Recently, the different viewpoints - focusing on lipids vs. proteins or physical vs. molecular driving forces for membrane organization - are increasingly converging. Here we review the basic properties of biological membranes and the most common theories for lateral segregation of membrane components before discussing an emerging model of a self-organized, multi-domain membrane or 'patchwork membrane'.     

Multifunctional plasma membrane redox systems

All the biological membranes contain oxidoreduction systems actively involved in their bioenergetics. Plasma membrane redox systems seem to be ubiquitous and they have been related to several important functions, including not only their role in cell bioenergetics, but also in cell defense through the generation of reactive oxygen species, in iron uptake, in the control of cell growth and proliferation and in signal transduction. In the last few years, an increasing number of mechanistic and molecular studies have deeply widened our knowledge on the function of these plasma membrane redox systems. The aim of this review is to summarize what is currently known about the components and physiological roles of these systems.     

Cell Physician: Reading Cell Motion

Cell motility is an essential phenomenon in almost all living organisms. It is natural to think that behavioral or shape changes of a cell bear information about the underlying mechanisms that generate these changes. Reading cell motion, namely, understanding the underlying biophysical and mechanochemical processes, is of paramount importance. The mathematical model developed in this paper determines some physical features and material properties of the cells locally through analysis of live cell image sequences and uses this information to make further inferences about the molecular structures, dynamics, and processes within the cells, such as the actin network, microdomains, chemotaxis, adhesion, and retrograde flow. The generality of the principals used in formation of the model ensures its wide applicability to different phenomena at various levels. Based on the model outcomes, we hypothesize a novel biological model for collective biomechanical and molecular mechanism of cell motion.     

Interaction of biological membranes with the cytoskeletal framework of living cells

The review is focused on the molecular structure and function of the proteins composing the actin-based cytokeletal cortex, located at the cytoplasmic face of plasma membranes of eucaryotic cells, which stabilizes integral membrane proteins in separate domains of cell membranes. It includes a survey of the molecular properties of teh proteins of the erythrocyte membrane skeleton such as spectrin, ankyrin, protein 4.1, and adducin. The properties of the immunological counterparts of erythroid cortical proteins found in nonerythroid tissues and cells are compared. The structural organization and function of the newly discovered class of calcium-binding proteins, nonerythroid peripheral membrane proteins, calpactins, are also described. Finally, the discussion of some experimental models illustrates that the membrane skeleton of living cells is actively involved in a wide variety of essential biological functions ranging from differentiation, to maintenance of cell polarity and cell shape, and regulation of exocytotic processes.     

Peptide conjugates as tools for the study of biological signal transduction

Today, many biological phenomena are being investigated and understood in molecular detail, and organic chemistry is increasingly being directed towards biological phenomena. This review is intended to highlight this interplay of organic chemistry and biology, using biological signal transduction as an example. Lipo-, glyco-, phospho- and nucleoproteins play key roles in the processes whereby chemical signals are passed across cell membranes and further to the cell nucleus. For the study of the biological phenomena associated with these protein conjugates, structurally well-defined peptides containing the characteristic linkage region of the peptide backbone with the lipid, the carbohydrate or the phosphoric acid ester can provide valuable tools. The multi-functionality and pronounced acid- and base-lability of such compounds renders their synthesis a formidable challenge to conventional organic synthesis. However, the recent development of enzymatic protecting groups, provides one of the central techniques which, when coupled with classic chemical synthesis, can provide access to these complex and sensitive biologically relevant peptide conjugates under particularly mild conditions and with high selectivity.     

排斥区研究综述

排斥区是指溶质分子在亲水界面附近被排斥而形成的一个几百微米区域,与普通的自由水相比,更加有序化,具有很多独特的理化特性,被认为是一种液晶态,即水的液态、固态、气态之外第四态。在生物学领域,如血管内皮细胞、植物根和肌肉等膜的亲水界面,也发现了排斥区。由于细胞膜的磷脂双分子层等亲水界面在生物体中广泛存在,生物体内细胞膜附近的区域很可能也是有序化的水,因此研究排斥区的各种物化性质对于理解和探索生命科学的本质具有重大意义,本身具有十分广阔的应用前景。在本文中,我们主要对排斥区的发现和发展历程进行综述,并从理化性质、结构特点和成因、受到光和电磁照射的影响以及在生物和医学领域的应用这几个方面做了详细描述和讨论,并对排斥区的特性进行了总结,对研究其的必要性进行了阐述,展望了它在生命科学研究中的应用前景。     

Tilted peptides: a motif for membrane destabilization (Hypothesis)

Cell life depends on the dynamics of molecular processes: molecule folding, organelle building and transformations involving membrane fusion, protein activation and degradation. To carry out these processes, the hydrophilic/hydrophobic interfaces of amphipathic systems such as membranes and native proteins must be disrupted. In the past decade, protein fragments acting in the disruption of interfaces have been evidenced: they are named the tilted or oblique peptides. Due to a peculiar distribution of hydrophobicity, they can disrupt hydrophobicity interfaces. Tilted peptides should be present in many proteins involved in various stages of cell life. This hypothesis overviews their discovery, describes how they are detected and discusses how they could be involved in dynamic biological processes.     

Nanobiotechnology: From Molecules to Systems

Nanobiotechnology is a key enabling multidisciplinary field for medical, technological and biological research and development, medicine, pharmaceutical development, and analytical sciences. Its foundation is the selective integration of a multitude of endeavours, such as biotechnology, chemical and physical nanotechnology, materials sciences, chemistry, engineering, electronics and optronics targeting the construction of micro‐ and nano‐arrays for analyzing complex mixtures of DNA, RNA, proteins, metabolites as well as the design of ultra‐sequencing devices, microbial fuel cells, implantates, molecular motors, artificial organs, and nanorobots. The developments in nanobiotechnology benefit from and contribute to the scientific advances in the chemical and physical nanotechnologies, in particular with respect to materials, composites, nanostructuring techniques, carbon nanotubes, and nanoelectronics.     

From mosaic to patchwork: Matching lipids and proteins in membrane organization

Abstract

Biological membranes encompass and compartmentalize cells and organelles and are a prerequisite to life as we know it. One defining feature of membranes is an astonishing diversity of building blocks. The mechanisms and principles organizing the thousands of proteins and lipids that make up membrane bilayers in cells are still under debate. Many terms and mechanisms have been introduced over the years to account for certain phenomena and aspects of membrane organization and function. Recently, the different viewpoints – focusing on lipids vs. proteins or physical vs. molecular driving forces for membrane organization – are increasingly converging. Here we review the basic properties of biological membranes and the most common theories for lateral segregation of membrane components before discussing an emerging model of a self-organized, multi-domain membrane or ‘patchwork membrane'.     

Tilted peptides: a motif for membrane destabilization (hypothesis)

Cell life depends on the dynamics of molecular processes: molecule folding, organelle building and transformations involving membrane fusion, protein activation and degradation. To carry out these processes, the hydrophilic/hydrophobic interfaces of amphipathic systems such as membranes and native proteins must be disrupted. In the past decade, protein fragments acting in the disruption of interfaces have been evidenced: they are named the tilted or oblique peptides. Due to a peculiar distribution of hydrophobicity, they can disrupt hydrophobicity interfaces. Tilted peptides should be present in many proteins involved in various stages of cell life. This hypothesis overviews their discovery, describes how they are detected and discusses how they could be involved in dynamic biological processes.     

Mechanisms of glycerophospholipid homeostasis in mammalian cells

The membranes of mammalian cells contain hundreds of different phospholipid species, a variety of glycolipids and cholesterol. While the reasons for such compositional diversity are not well established, they probably relate to a multitude of membrane-associated functions each of which sets specific requirements for the chemical and physical properties of membranes. The lipid composition of membranes must therefore be accurately controlled. The maintenance of phospholipid homeostasis in a mammalian cell is a daunting task due to presence of many phospholipid (and other lipid) classes and hundreds of different molecular species. In addition, the phospholipid composition of the cellular membranes depends on several different phenomena including biosynthesis, remodelling, degradation and interorganelle trafficking. Accordingly, it is not surprising that phospholipid homeostasis in mammalian cells is poorly understood. Particularly little is known about the regulation and coordination of processes contributing to homeostasis. Nevertheless, it has become obvious that selective degradation plays a major role, albeit the enzymes involved remain to be discovered. Beside the complexity of the phenomenon, methodological limitations have hampered the progress in this field. Here, we review the key features of the processes contributing to phospholipid homeostasis in mammalian cells, with a particular emphasis on the regulation and coordination of biosynthesis and degradation.     

A turbo engine with automatic transmission? How to marry chemicomotion to the subtleties and robustness of life

Most genomes are much more complex than required for the minimum chemistry of life. Evolution has selected sophistication more than life itself. Could this also apply to bioenergetics? We first examine mechanisms through which bioenergetics could deliver sophistication. We illustrate possible benefits of the turbo-charging of catabolic pathways, of loose coupling, low-gear catabolism, automatic transmission in energy coupling, and of homeostasis. Mechanisms for such phenomena may reside at the level of individual proton pumps, or consist of rerouting of electrons over parallel pathways. The mechanisms may be confined to preexisting components, or involve the plasticity of gene expression that is so characteristic of most living organisms. These possible benefits lead us to the conjecture that also bioenergetics has evolved more for sophistication than for necessity. We next discuss a hitherto unresolved enigma, i.e. that bioenergetics does not seem to be critical for the physiological state. To decide on how critical bioenergetics is, we quantified the control exerted by catabolism on important physiological functions such as growth rate and growth yield. We also determined whether a growth inhibition mostly affected bioenergetics (catabolism) or anabolism; if ATP increases with growth rate, then growth should be considered energy (catabolism) limited. The experimental results for Escherichia coli pinpoint the enigma: its energy metabolism (catabolism) is not critical for growth rate. These results might suggest that because it has no direct control over cell function, bioenergetics is unimportant. Paradoxically however, in biology, highly important mechanisms tend to have little control on cell function, precisely because of that importance. Sophistication in terms of homeostatic mechanisms has evolved to guarantee robustness of the most important functions: The most important mechanisms are redundant in biology. Bioenergetics may be an excellent example of this paradox, in line with the above conjecture. It may be highly important and sophisticated. We then discuss work that has begun to focus on the sophistication of bioenergetics. Homeostasis of the energetics of DNA structure in E. coli is extensive. It relies both on preexisting components and on responsive gene expression. The vastly parallel electron-transfer network of Paracoccus denitrificans engages in sophisticated dynamic and hierarchical regulation. The growth yield of the organism can depend on which terminal oxidases are active. Effective proton translocation may vary due to rerouting of electrons. We conclude that much sophistication of bioenergetics will be discovered in this era of functional genomics.     

Self-assembly of reactive amphiphilic block copolymers as mimetics for biological membranes

Over the years, polymers have attracted a great deal of interest because they offer a unique platform for the development of materials in fields as diverse as biomedicine and packaging. Many of these purposes use polymers that had been developed for totally different applications. Recently, however, chemical tailoring and molecular and supramolecular control of the chemistry and, thus, the physical and biological response have become a key interest of many researchers. In particular, systems that operate in aqueous media have become an intensely researched field. This is mostly because many devices must be biocompatible, which implies that they have to function in aqueous solutions. Over the past few years, new approaches for mimicking cell surfaces, for generating biocompatible and bioactive drug delivery systems, and for directed targeting have been developed. One recent development is polymeric systems with an enhanced biofunctionality, such as amphiphilic block copolymers that can act as mimetics for biological membranes. Because there are virtually no limits to combinations of monomers, biological and synthetic building blocks, ligands, receptors, and other proteins, polymer hybrid materials show a great promise for applications in biomedicine and biotechnology.