基于结构分类的蛋白质折叠模式识别方法

对用于折叠模式识别的蛋白质结构数据库进行结构分类,构建了四个分类库：Ａｌ－α库,Ａｌ－β库,α／β库,α＋β库和一个总库,然后分别统计出不同灵敏度的匹配评估函数（平均势）。对不同的平均势,不同结构类型的蛋白进行的检验发现：来源于α／β库的平均势预测能力最强,来源于Ａｌ－α库的平均势预测能力最弱;对α／β蛋白的预测成功率最高,对Ａｌ－α蛋白的预测成功率最低。这与α／β蛋白结构最规则,Ａｌ－α蛋白未加入辅基不能反映出结构的全部特征是相一致的     

On Exact Unconditional Test for Linear Trend in Dose‐Response Studies

The one‐degree‐of‐freedom Cochran‐Armitage (C‐A) test statistic for linear trend has been widely applied in various dose‐response studies (e.g., anti‐ulcer medications and short‐term antibiotics, animal carcinogenicity bioassays and occupational toxicant studies). This approximate statistic relies, however, on asymptotic theory that is reliable only when the sample sizes are reasonably large and well balanced across dose levels. For small, sparse, or skewed data, the asymptotic theory is suspect and exact conditional method (based on the C‐A statistic) seems to provide a dependable alternative. Unfortunately, the exact conditional method is only practical for the linear logistic model from which the sufficient statistics for the regression coefficients can be obtained explicitly. In this article, a simple and efficient recursive polynomial multiplication algorithm for exact unconditional test (based on the C‐A statistic) for detecting a linear trend in proportions is derived. The method is applicable for all choices of the model with monotone trend including logistic, probit, arcsine, extreme value and one hit. We also show that this algorithm can be easily extended to exact unconditional power calculation for studies with up to a moderately large sample size. A real example is given to illustrate the applicability of the proposed method.     

Unveiling the Microscopic Origin of Irreversible Capacity Loss of Hard Carbon for Sodium-Ion Batteries

The primary bottleneck hindering the application of hard carbon in sodium-ion batteries (SIBs) anodes lies in its inadequate initial Coulombic efficiency (ICE). Unclear causes of capacity loss at the microscopic level restrict the improvement of hard carbon anodes. Here, two pivotal stages that influence the structure and composition of hard carbon, namely synthesis, and storage are evaluated; subsequently identifying crucial determinants contributing to irreversible capacity loss. The results suggest that undergrown carbon layers allowing the intrusion of solvent molecules into the interior of the hard carbon is a key factor during the synthesis stage, while the gradual formation of oxygen-containing functional groups on the surface of the hard carbon is another factor leading to irreversible loss of capacity during storage stage. This research microscopically clarifies the irreversible capacity loss mechanism on hard carbon and provides guidelines for designing and applying high ICE hard carbon for SIBs.     

Identification of mitogen-activated protein kinase-activated protein kinase-2 as a vimentin kinase activated by okadaic acid in 9L rat brain tumor cells

Organization of intermediate filament, a major component of cytoskeleton, is regulated by protein phosphorylation/dephosphorylation, which is a dynamic process governed by a balance between the activities of involved protein kinases and phosphatases. Blocking dephosphorylation by protein phosphatase inhibitors such as okadaic acid (OA) leads to an apparent activation of protein kinase(s) and to genuine activation of phosphatase-regulated protein kinase(s). Treatment of 9L rat brain tumor cells with OA results in a drastically increased phosphorylation of vimentin, an intermediate filament protein. In-gel renaturing assays and in vitro kinase assays using vimentin as the exogenous substrate indicate that certain protein kinase(s) is activated in OA-treated cells. With specific protein kinase inhibitors, we show the possible involvement of the cdc2 kinase- and p38 mitogen-activated protein kinase (p38^MAPK)-mediated pathways in this process. Subsequent in vitro assays demonstrate that vimentin may serve as an excellent substrate for MAPK-activated protein kinase-2 (MAPKAPK-2), the downstream effector of p38^MAPK, and that MAPKAPK-2 is activated with OA treatment. Comparative analysis of tryptic phosphopeptide maps also indicates that corresponding phosphopeptides emerged in vimentin from OA-treated cells and were phosphorylated by MAPKAPK-2. Taken together, the results clearly demonstrate that MAPKAPK-2 may function as a vimentin kinase in vitro and in vivo. These findings shed new light on the possible involvement of the p38^MAPK signaling cascade, via MAPKAPK-2, in the maintenance of integrity and possible physiological regulation of intermediate filaments. J. Cell. Biochem. 71:169–181, 1998. © 1998 Wiley-Liss, Inc.     

Focus: Rare Disease: Prostatic Schwannoma Presenting with Prostate-specific Antigen Elevation: A Case Report

Introduction: Schwannoma of the male genital system is very uncommon and is mostly treated by surgery. However, prostatic schwannoma presenting with elevated prostate-specific antigen (PSA) level and treated conservatively are extremely rare. Case presentation: Herein, we present a rare case of a prostatic schwannoma in a 65-year-old man who initially presented with an elevated PSA level. Digital rectal examination revealed an enlarged prostate with a palpable hard nodule on the left side. Transrectal ultrasonography revealed an enlarged prostate with a well-defined homogeneously hypoechoic nodule in the left peripheral lobe. Biopsy was done, and histopathology revealed a prostatic schwannoma. Conservative treatment with regular image follow-up was done per the patient’s preference. Mild PSA progression but no worsening of symptoms was found in 6 years of follow-up. Conclusions: PSA elevation could be a rare presentation of prostatic schwannoma. Treatment options other than surgery, such as conservative treatment with close observation, could be feasible for these rare tumors and long-term survivorship can be achieved.     

Cyclic pentapeptides of chiral sequence DLDDL as scaffold for antagonism of G‐protein coupled receptors: Synthesis,activity and conformational analysis by NMR and molecular dynamics of ITF 1565 a substance P inhibitor

Under the hypotheses of a structurally related binding site for antagonists of G‐protein coupled receptors and the ability of cyclic pentapeptides of chiral sequence D ¹L ²D ³D ⁴L ⁵ to form rigid structures with which probe the pharmacophoric specificity of these receptors, inhibitors of substance P were designed based on available structure–activity relationships. ITF 1565, cyclo[D ‐Trp¹‐Pro²‐D ‐Lys³‐D ‐Trp⁴‐Phe⁵], antagonized substance P activity mediated by type 1 neurokinin receptor (NK1) whereas it acted weakly against NK2 and did not inhibit endothelin at all. The preferential conformation of the peptide was obtained from nmr spectroscopy and computer calculations, and shown to contain the same βII‐turn and γ′‐turn found in other cyclic pentapeptides with the same chiral sequence. The structure of the peptide was compared with that of the β‐D ‐glucose molecule that has been proposed as a semirigid scaffold for antagonists of G‐protein coupled receptors. The γ′‐turn of the cyclic peptide superimposed well with β‐D ‐glucose in the chair conformation. Furthermore, when the side chains were considered, the aromatic groups of the two molecules were found to generally overlap. These results support the view of G‐protein coupled receptors as possessing structurally similar binding sites for antagonists and suggest that cyclic pentapeptides of chiral sequence D ¹L ²D ³D ⁴L ⁵ may be useful as semirigid scaffolds for the design of antagonists of this family of receptors. © 1999 John Wiley & Sons, Inc. Biopoly 50: 211–219, 1999     

Macrocyclic inhibitors of Factor XIa: Discovery of alkyl-substituted macrocyclic amide linkers with improved potency

Optimization of macrocyclic inhibitors of FXIa is described which focused on modifications to both the macrocyclic linker and the P1 group. Increases in potency were discovered through interactions with a key hydrophobic region near the S1 prime pocket by substitution of the macrocyclic linker with small alkyl groups. Both the position of substitution and the absolute stereochemistry of the alkyl groups on the macrocyclic linker which led to improved potency varied depending on the ring size of the macrocycle. Replacement of the chlorophenyltetrazole cinnamide P1 in these optimized macrocycles reduced the polar surface area and improved the oral bioavailability for the series, albeit at the cost of a decrease in potency.