Related papers: Evolution of Two Membrane Protein Sequences and Fu…
The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises…
Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
We focus here on the scaling properties of small interspecies differences between red cone opsin transmembrane proteins, using a hydropathic elastic roughening tool previously applied to the rhodopsin rod transmembrane proteins. This tool…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
Recent advances in machine learning have become increasingly popular in the applications of phase transitions and critical phenomena. By machine learning approaches, we try to identify the physical characteristics in the two-dimensional…
Motivation: Human cancer is caused by the accumulation of somatic mutations in tumor suppressors and oncogenes within the genome. In the case of oncogenes, recent theory suggests that there are only a few key "driver" mutations responsible…
T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is a central component of adaptive immunity, with implications for vaccine design, cancer immunotherapy, and autoimmune disease. While recent advances in machine learning…
I believe an atomic biology is needed to supplement present day molecular biology, if we are to design and understand proteins, as well as define, make, and use them. Topics in the paper are molecular biology and atomic biology.…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such…
We describe simulations of Proteins and artificial pseudo-molecules interacting and shaping lipid bilayer membranes. We extract protein diffusion Parameters, membrane deformation profiles and the elastic properties of the used membrane…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++,…
Identification of critical residues of a protein is actively pursued, since such residues are essential for protein function. We present three ways of recognising critical residues of an example protein, the evolution of which is tracked…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
Cells of diatoms and related algae with complex plastids of red algal origin are highly compartmentalized. These plastids are surrounded by four envelope membranes, which also define the periplastidic compartment (PPC), the space between…
Biological membranes mainly consist of lipids and proteins. While the proteins have many functions as single molecules, the membrane as a whole displays physical properties that cannot be explained on the single molecule level. For example,…
It is established that prion protein is the sole causative agent in a number of diseases in humans and animals. However, the nature of conformational changes that the normal cellular form PrPC undergoes in the conversion process to a…