Related papers: Evolution of Two Membrane Protein Sequences and Fu…
Because of their large size and widespread mechanosensitive interactions the only recently discovered titled transmembrane proteins have attracted much attention. Here we present and discuss their hydropathic profiles using a new method of…
T-cell receptor (TCR) interactions with antigenic peptides underpin adaptive immunity and are pivotal for personalized immunotherapy and vaccine development. Despite recent progress, computational modeling of TCR-peptide specificity remains…
T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies. Modeling the distribution of TCR sequences is of…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
Structural Maintenance of Chromosomes, SMCs, proteins have long rod like structures immersed in water. Here we use our hydroanalytic methods based on amino acid sequences to discuss their dynamics at multiple length scales identified by…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called $\alpha$ and $\beta$, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human…
Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenges…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
Rhodopsin is a G-protein coupled receptor found in retinal rod cells, where it mediates monocrhromatic vision in dim light. It is one of the most studied proteins with thousands of reviewed entries in Uniprot. It has seven transmembrane…
The recognition of essential proteins not only can help to understand the mechanism of cell operation, but also help to study the mechanism of biological evolution. At present, many scholars have been discovering essential proteins…
The complex nature of tripartite peptide-MHC-TCR interactions is a critical yet underexplored area in immunogenicity prediction. Traditional studies on TCR-antigen binding have not fully addressed the complex dependencies in triad binding.…
Plasma membrane tubes are ubiquitous in cellular membranes and in the membranes of intracellular organelles. They play crucial roles in trafficking, ion transport, and cellular motility. The formation of plasma membrane tubes can be due to…
Membrane proteins are crucial in regulating biomembrane shapes and controlling the dynamic changes in membrane morphology during essential cellular processes. These proteins can localize to regions with their preferred curvatures (curvature…
In this article we compare electrical conductance events from single channel recordings of three TRP channel proteins (TRPA1, TRPM2 and TRPM8) expressed in human embryonic kidney cells with channel events recorded on synthetic lipid…
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are…
Membranes are of great technological and biological as well as theoretical interest. Two main classes of membranes can be distinguished: Fluid membranes and polymerized, tethered membranes. Here, we review progress in the theoretical…
Protein circular permutations are crucial for understanding protein evolution and functionality. Traditional detection methods, sequence-based or structure-based, struggle with accuracy and computational efficiency, the latter also limited…