Despite major advances in T cell receptor (TCR) biology and structure, how peptide-MHC complex (pMHC) ligands trigger αβ TCR activation remains unresolved. Two views exist. One model postulates that monomeric TCR-pMHC ligation events are sufficient while a second proposes that TCR-TCR dimerization in cis via Cα domain interaction plus pMHC binding is critical. We scrutinized 22 known TCR/pMHC c...

The genes PRKACA and PRKACB encode the principal catalytic (C) subunits of protein kinase A (PKA) Cα and Cβ, respectively. Cα is expressed in all eukaryotic tissues examined and studies of Cα knockout mice demonstrate a crucial role for Cα in normal physiology. We have sequenced exon 2 through 10 of PRKACA from the genome of 498 Norwegian donors and extracted information about PRKACA mutations ...

Λ:λրΛ(cα(b) + u)(cα(b) + v)κα(λ,Λ)φ(Λ) = (nα + uv) φ(λ), where cα(b) is the α-content of a new box b = Λ \ λ. If α = 1, this identity implies the existence of an interesting family of positive definite central functions on the infinite symmetric group. The approach is based on the interpretation of a Young diagram as a pair of interlacing sequences, so that analytic techniques may be used to so...

Cyclic peptide nanotubes (CPNTs) formed by the self-assembly of cyclic peptides (CPs) with an even number of alternate l/d amino acids are typically used in the field of the transport of ions and drug molecules across the lipid bilayer. This study investigates the transport mechanism of the antitumor drug molecule, 5-fluorouracil (5FU), through the CPNT using classical and steered molecular dyn...

We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman ...

We introduce the weak partial square principles pλ,κ and p λ,<κ, which combine the ideas of a weak square sequence and a partial square sequence. We construct models in which weak partial square principles fail. The main result of the paper is that λ,κ does not imply λ,<κ. Let λ be a regular uncountable cardinal and let κ ≤ λ be a nonzero cardinal. Recall the square principle λ,κ (respectively ...

Free radical-initiated peptide sequencing (FRIPS) mass spectrometry derives advantage from the introduction of highly selective low-energy dissociation pathways in target peptides. An acetyl radical, formed at the peptide N-terminus via collisional activation and subsequent dissociation of a covalently attached radical precursor, abstracts a hydrogen atom from diverse sites on the peptide, yiel...

This article is concerned with characteristic Sturmian words of slope α and 1−α (denoted by cα and c1−α respectively), where α ∈ (0, 1) is an irrational number such that α = [0; 1 + d1, d2, . . . , dn] with dn ≥ d1 ≥ 1. It is known that both cα and c1−α are fixed points of non-trivial (standard) morphisms σ and σ̂, respectively, if and only if α has a continued fraction expansion as above. Accor...

Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary s...

Accurate predictions of the amount and the rate of long- term deformation of reinforced soils under an applied load are important key issue in geotechnical engineering, in which the deformation of soil develops with time at a state of constant effective stress. Since geosynthetic is generally considered creep sensitive therefore, evaluation of creep behavior of geosynthetic reinforced soil (GRS...