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A novel multifunctional nanoreactor was designed for highly efficient detection and profiling of membrane proteins using macroporous siliceous foams (MSF) with large pore size of ∼ 70 nm and hydrophobic surface (contact angle over 100°). By introducing organo groups (e. g. from bis(triethoxysilyl)ethane) on the surface of MSF, the modified material was employed for selective extraction and in situ...
Membrane proteins embedded in bi-layer lipids of cell membrane have unique functions including inter-cell communication, ions/molecules transport. And there is more than 50% of drug design emphasizes on membrane proteins specifically studying on their structure and formation. Recently we reported the structural and functional studies of membrane protein lipid nanoparticles in native biological membrane...
The increasing protein sequences from the genome project require theoretical methods to predict transmembrane helical segments (TMHs). In this paper, a method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1F88 is chosen as an example to describe the prediction process with this method. One group of test data...
The potentialities of the atomic force microscopy (AFM) make it a tool of the undeniable value for the study of biomolecule samples. One of the main steps for the application of atomic force microscopy to the study of proteins has been the self-assembled monolayers (SAMs). The methods of physical adsorption and chemical modification are utilized to immobilize proteins to substrates efficiently. SAMs...
Membrane-bound macromolecules play an important role in tissue architecture and cell-cell communication, and is regulated by almost one-third of the genome. At the optical scale, one group of membrane proteins expresses themselves as linear structures along the cell surface boundaries, while others are sequestered. This paper targets the former group, whose intensity distributions are often heterogeneous...
Our objective is to develop a highly miniaturized, solid-phase platform for assaying the function and inhibition of integral membrane proteins (IMPs). To functionalize materials with active membrane proteins, the challenge is to build stabilized, supported biomembranes in which the substrate to biomembrane spacing can be controlled to accommodate larger membrane protein. The silica microsphere (5...
Our aim is to design alpha-helical peptide complexes to enhance their stability and biological feasibility for the study of membrane proteins and their interactions. In on-going work, we employ (K3A4L2A7L2A3K3) as anchoring molecules, where conjugation of the peptide with fluoresceine isothiocyanate (FITC) allows one to access a variety of chemistries (such as introducing fluorescent dye, etc.) for...
In this work we for the first time demonstrate real-time monitoring of the expression of membrane proteins in native, live cells, free of hydrodynamic stress at single cell resolution. This micro-optofluidic mechanism is uniquely enabled by the intricate interplay of gravity induced sedimentation with laminar flow, fast diffusion and short optical path length on our lab-in-a-trench platform.
Membrane protein interactions are involved in the regulation and execution of all biochemical pathways within the cell. It is crucial to identify the binding partners for understanding the function of an uncharacterized protein, and when these partners turn out to have known function, deductions about the potential role of the uncharacterized protein can often be made. However, the analysis of interactions...
A novel bottom-gate top-contact OTFT architecture has been fabricated. In this device, a lipid bilayer structure embedding a photosynthetic membrane protein extracted from Rhodobacter Sphaeroides has been deposited onto the organic semiconductor film (alpha,omega-dihexylsexythiophene) prior to the evaporation of source and drain gold contacts. The figures of merit of this device were extracted and...
To overcome the photobleaching problem inherent to fluorescence techniques we recently developed a new optical detection method for individual non-fluorescent nano-objects. It allows detecting the movement of individual membrane proteins labeled with 5 nm gold nanoparticles in living cells for arbitrary long times.
Membrane proteins are an important class of proteins that serve as channels, receptors, and energy transducers in a cell membrane. Knowledge of a given type of cell membrane protein is crucial for determining its function. This paper introduces an automated, in-silico method for identifying different types of membrane proteins based on their amino acid composition. Our method applies a novel, composite...
Membrane proteins organize themselves in a linear fashion where adjacent cells are attached together along the basal-lateral region. Their intensity distributions are often heterogeneous and may lack specificity. Grouping of these linear structures can aid in segmentation and quantitative representation of protein localization. However, quantitative analysis of these signals is often hindered by noise,...
Giant unilamellar vesicles (GUVs) are biochemical compartments enclosed with phospholipid bilayers. GUVs are expected to be materials for construction and investigation of artificial cell models. There, fusion phenomena between GUVs and smaller vesicles (referred to as "asymmetric fusion" here) seem to have some potential for utilization of the transporters bringing reagents and membrane...
Electrochemical impedance spectroscopy (EIS) is a powerful tool for characterizing biological materials, including lipid bilayers and many membrane proteins. However, traditional EIS methods are very slow at low frequencies, where these materials respond in biosensor applications. To enable dense arrays of biosensors based on tethered bilayer lipid membranes (tBLM), a new approach for EIS has been...
In the early seventies, it was clear that primary amino acid sequence and its local solution environment hold most of the information necessary for protein folding. Since then, scientists have been trying to solve the bioinformatics problem by constructing the tertiary three-dimensional structure of protein from the primary amino acid sequences by using computational biology. Success of several genome...
Molecular biology works at the nanoscale with most cellular processes depending on complexes of proteins, DNA and membranes that have dimensions in the range 1-100 nm. In order to interface with biology any physical device should present biological components which are ordered on this scale. To achieve this control we must resort to bottom-up methods of manufacturing and this requires that the biological...
Many of the central questions in bioinformatics relate to protein structure and function. We are mainly be concerned with three problems: identifying transmembrane segments in proteins, distinguishing disordered from ordered regions, and determining protein function from sequence information. In order to deal effectively with these problems, we have conducted an in-depth analyses of the physiochemical...
Advances in genome sequencing technology have led to an exploration in the amount of sequence data available, learning from proteins coded for by genomes is a difficult task. Bioinformatics is thus a burgeoning field that holds great promise for deepening our understanding of biochemical pathways, for understanding the genetic differences between species and how they arose, and for understanding the...
Tethered bilayer lipid membranes (tBLMs) present a powerful kind of solid supported membranes that can be used to study membrane related processes. TBLMs offer a quasi-natural environment where membrane proteins can be embedded and investigated. A tBLM consists of a lipid bilayer that is coupled covalently via a spacer group to a solid support. This being an electrode, electrical characterization...
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