There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Computational Prediction of 1H and 13C Chemical Shifts: A Useful Tool for Natural Product, Mechanistic, and Synthetic Organic Chemistry

Constructing highly planar, extended π-electron systems is an important strategy for achieving high-mobility organic semiconductors. In general, there are two synthetic strategies for achieving π-conjugated systems with high planarity. The conventional strategy connects neighboring aromatic rings through covalent bonds to restrict the rotation about single bonds. However, this usually requires a complex sequence of synthetic steps to achieve this target, which can be costly and labor-intensive. More recently, noncovalent through-space intramolecular interactions, which are defined here as noncovalent conformational locks, have been employed with great success to increase the planarity and rigidity of extended π-electron systems; this has become a well-known and important strategy to design and synthesize highly planar π-conjugated systems for organic electronics. This review offers a comprehensive and general summary of conjugated systems with such noncovalent conformational locks, including O···S, N···S,...

Organic and Polymeric Semiconductors Enhanced by Noncovalent Conformational Locks.

We study apo and holo forms of the bacterial ferric binding protein (FBP) which exhibits the so-called ferric transport dilemma: it uptakes iron from the host with remarkable affinity, yet releases it with ease in the cytoplasm for subsequent use. The observations fit the “conformational selection” model whereby the existence of a weakly populated, higher energy conformation that is stabilized in the presence of the ligand is proposed. We introduce a new tool that we term perturbation-response scanning (PRS) for the analysis of remote control strategies utilized. The approach relies on the systematic use of computational perturbation/response techniques based on linear response theory, by sequentially applying directed forces on single-residues along the chain and recording the resulting relative changes in the residue coordinates. We further obtain closed-form expressions for the magnitude and the directionality of the response. Using PRS, we study the ligand release mechanisms of FBP and support the findings by molecular dynamics simulations. We find that the residue-by-residue displacements between the apo and the holo forms, as determined from the X-ray structures, are faithfully reproduced by perturbations applied on the majority of the residues of the apo form. However, once the stabilizing ligand (Fe) is integrated to the system in holo FBP, perturbing only a few select residues successfully reproduces the experimental displacements. Thus, iron uptake by FBP is a favored process in the fluctuating environment of the protein, whereas iron release is controlled by mechanisms including chelation and allostery. The directional analysis that we implement in the PRS methodology implicates the latter mechanism by leading to a few distant, charged, and exposed loop residues. Upon perturbing these, irrespective of the direction of the operating forces, we find that the cap residues involved in iron release are made to operate coherently, facilitating release of the ion.

/pdf/perturbation-response-scanning-reveals-ligand-entry-exit-31uynxsikd.pdf

Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein.

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories

MD-TASK: a software suite for analyzing molecular dynamics trajectories.

Intramolecular interactions of noncovalent nature in the conjugated oligomers of co-thiophene−thieno[3,4-b]pyrazine−thiophene and co-thiophene−benzo[c]1,2,5-thiadiazole−thiophene are studied quantum mechanically. S···N contacts are identified by the existence of topological bond critical points (bcp's) along the bond path by means of atoms-in-molecules (AIM) theory. The planarity of the oligomers is attributed to the observed ring critical points among the thiophene and pyrazine or thiadiazole rings. Similar systems, obtained by replacing the thiophene by pyrrole and pyrazine by ethylenedioxy, are further studied with AIM analysis. The extent of the contribution of intramolecular interactions to the intrinsic conductivity of the conjugated polymers is investigated by extrapolating the oligomer band gap values from the time-dependent density functional theory excitation energies and density functional theory HOMO−LUMO gaps and is found to be in excellent agreement with measured experimental values, where v...

Canan Atilgan

Papers

Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein.

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

MD-TASK: a software suite for analyzing molecular dynamics trajectories.

Noncovalent Intramolecular Interactions in the Monomers and Oligomers of the Acceptor and Donor Type of Low Band Gap Conducting Polymers

Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication.