抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

In the United States over 1.7 million cases of traumatic brain injury are reported yearly, but predictive correlation of cellular injury to impact tissue strain is still lacking, particularly for neuronal injury resulting from compression. Given the prevalence of compressive deformations in most blunt head trauma, this information is critically important for the development of future mitigation and diagnosis strategies. Using a 3D in vitro neuronal compression model, we investigated the role of impact strain and strain rate on neuronal lifetime, viability, and pathomorphology. We find that strain magnitude and rate have profound, yet distinctively different effects on the injury pathology. While strain magnitude affects the time of neuronal death, strain rate influences the pathomorphology and extent of population injury. Cellular injury is not initiated through localized deformation of the cytoskeleton but rather driven by excess strain on the entire cell. Furthermore we find that, mechanoporation, one of the key pathological trigger mechanisms in stretch and shear neuronal injuries, was not observed under compression.

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Strain and rate-dependent neuronal injury in a 3D in vitro compression model of traumatic brain injury

Single-sequence protein structure prediction using a language model and deep learning

The Yang-Baxter equation has long been recognised as the masterkey to integrability, providing the basis for exactly solved models which capture the fundamental physics of a number of realistic classical and quantum systems. In this article we provide an introductory overview of the impact of Yang-Baxter integrable models on experiments in condensed matter physics and ultracold atoms. A number of prominent examples are mentioned, including the hard-hexagon model, the Heisenberg spin chain, the transverse quantum Ising chain, a spin ladder model, the Lieb-Liniger Bose gas, the Gaudin-Yang Fermi gas and the two-site Bose-Hubbard model. The review concludes by pointing to some other recent developments with promise for further progress.

Yang-Baxter integrable models in experiments: from condensed matter to ultracold atoms

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into ‘cumulus-type’, i.e., those similar to puffy (white) clouds, and ‘stratus-type’, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an ‘energy transfer’ mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by ‘multi-trajectories’; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach ‘rarely visited’ but functionally-related states. We also show the role of disorder in ‘spatial games’ of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks

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Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review.

We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three-dimensional space. Our approach is based on the concept of an intrinsically discrete cur ...

Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins

We introduce a novel generalization of the discrete nonlinear Schrodinger equation. It supports solitons that we utilize to model chiral polymers in the collapsed phase and, in particular, proteins in their native state. As an example we consider the villin headpiece HP35, an archetypal protein for testing both experimental and theoretical approaches to protein folding. We use its backbone as a template to explicitly construct a two-soliton configuration. Each of the two solitons describe well over 7.000 supersecondary structures of folded proteins in the Protein Data Bank with sub-angstrom accuracy suggesting that these solitons are common in nature.

Discrete nonlinear Schrödinger equation and polygonal solitons with applications to collapsed proteins.

In this paper, several proposals of optically simulating Yang-Baxter equations have been presented. Motivated by the recent development of anyon theory, we apply Temperley-Lieb algebra as a bridge to recast a four-dimensional Yang-Baxter equation into its two-dimensional counterpart. In accordance with both representations, we find the corresponding linear-optical simulations, based on the highly efficient optical elements. Both the degrees of freedom of photon polarization and location are utilized as the qubit basis, in which the unitary Yang-Baxter matrices are decomposed into a combination of actions of basic optical elements.

Optical simulation of the Yang-Baxter equation

We argue that protein loops can be described by topological domain-wall solitons that interpolate between ground states which are the alpha helices and beta strands. We present an energy function that realizes loops as soliton solutions to its equation of motion, and apply these solitons to model a number of biologically active proteins including 1VII, 2RB8, and 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to numerically construct soliton solutions that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 1.0 angstrom or less for the central alpha-carbons, i.e., close to the limits of current experimental accuracy.

/pdf/topological-solitons-and-folded-proteins-2oxu1u85pt.pdf

Topological solitons and folded proteins

In all-atom molecular simulation studies of proteins, each atom in the protein is represented by a point mass and interactions are defined in terms of the atomic positions. In recent years, various simplified approaches have been proposed. These approaches aim to improve computational efficiency and to provide a better physical insight. The simplified models can differ widely in their description of the geometry and the interactions inside the protein. This study explores the most fundamental choice in the simplified protein models: the choice of a coordinate set defining the protein structure. A simplified model can use fewer point masses than the all-atom model and/or eliminate some of the internal coordinates of the molecule by setting them to an average or ideal value. We look at the implications of such choices for the overall protein structure. We find that care must be taken for angular coordinates, where even very small variations can lead to significant changes in the positions of far away atoms. In particular, we show that the ϕ/ψ torsion angles are not a sufficient coordinate set, whereas another coordinate set with two degrees of freedom per residue, virtual Cα backbone bond, and torsion angles performs satisfactorily.

Shuangwei Hu

Papers

Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins

Discrete nonlinear Schrödinger equation and polygonal solitons with applications to collapsed proteins.

Optical simulation of the Yang-Baxter equation

Topological solitons and folded proteins

A comparison of reduced coordinate sets for describing protein structure