Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.     

Multifunctional land‐use value mapping and space type classification: A case study of Puge County,China

Land exhibits diverse functions under the combined influence of natural and human forces. A production–living–ecology functional classification system was constructed by integrating land, ecosystem, and landscape functions. The land functional value was calculated by systematically integrating ecosystem service value assessments. The primary and secondary functions, as well as combinations of different land‐use types, were determined using vertical and horizontal comparison methods. The production–living–ecology ranges were then delineated in Puge County, which is a typical mountain county in China. The production–living–ecology functions identified were well connected with the current land‐use types. The “production–living–ecology” space in Puge County showed obvious multifunctionality and agglomeration. The function identification system proposed in this paper integrated multiple methods, overcame the difficulty of direct quantitative identification of land functions. The methods used to map and quantify land function will enhance our ability to understand and model land system changes and adequately inform policies and planning. Summary for Managers

• The function valuation method constructed in this paper could be used to reflect the multifunctionality and importance of land use and provide guidance and a quantitative basis for regional development planning.
• The spatial classification results provided in this paper could offer a valuable reference for the land management department to scientifically formulate land use planning.
• Under the goal of creating a group‐type urban development pattern and constructing an ecological protection pattern in Puge County, the hotspot analysis results of this paper can provide decision‐making tools and alternative spatial plans.

     

Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm

The Transition Rapidly exploring Random Eigenvector Assisted Tree (TRREAT) algorithm is introduced to perform searches along low curvature pathways on a potential energy surface (PES). The method combines local curvature information about the PES with an iterative Rapidly exploring Random Tree algorithm (LaValle, Computer Science Department, Iowa State University, 1998, TR98–11) that quickly searches high‐dimensional spaces for feasible pathways between local minima. Herein, the method is applied to identifying conformational changes of molecular systems using Cartesian coordinates while avoiding a priori definition of collective variables. We analyze the pathway identification problem for alanine dipeptide, cyclohexane and glycine using nonreactive and reactive forcefields. We show how TRREAT‐identified pathways can be used as valuable input guesses for double‐ended methods such as the Nudged Elastic Band when ascertaining transition state energies. This method can be utilized to improve/extend the reaction databases that lie at the core of automatic chemical reaction mechanism generator software currently developed to build kinetic models of chemical reactions. © 2013 Wiley Periodicals, Inc.     

Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc.     

On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

Mdm2生成速率调控的p53-Mdm2振子的全局动力学和稳定性

肿瘤抑制蛋白p53的动力学在一定程度上可以决定DNA损伤后的细胞命运.p53的动力学行为与p53信号通路中p53-Mdm2振子模块密切相关.然而,p53的负调控子Mdm2的生成速率的增加使其在一些癌细胞中过表达.因此探讨Mdm2生成速率对p53动力学的影响有重要意义.同时,PDCD5作为p53的激活子也调控p53的表达.因此,本文针对PDCD5调控的p53-Mdm2振子模型,通过分岔分析获得了Mdm2生成速率所调控的p53的单稳态、振荡以及单稳态与振荡共存的动力学行为,且稳定性通过能量面进行了分析.此外,噪声强度对p53动力学的稳定性有重要的影响.因此,针对p53的振荡行为,探讨了噪声强度对势垒高度和周期的影响.本文所获得的结果对理解DNA损伤后的p53信号通路调控起到一定的指导作用.     

Combinatorial Crystal Synthesis: Structural Landscape of Phloroglucinol:1,2‐bis(4‐pyridyl)ethylene and Phloroglucinol:Phenazine

A large number of crystal forms, polymorphs and pseudopolymorphs, have been isolated in the phloroglucinol‐dipyridylethylene (PGL:DPE) and phloroglucinol‐phenazine (PGL:PHE) systems. An understanding of the intermolecular interactions and synthon preferences in these binary systems enables one to design a ternary molecular solid that consists of PGL, PHE, and DPE, and also others where DPE is replaced by other heterocycles. Clean isolation of these ternary cocrystals demonstrates synthon amplification during crystallization. These results point to the lesser likelihood of polymorphism in multicomponent crystals compared to single‐component crystals. The appearance of several crystal forms during crystallization of a multicomponent system can be viewed as combinatorial crystal synthesis with synthon selection from a solution library. The resulting polymorphs and pseudopolymorphs that are obtained constitute a crystal structure landscape.     

大型综合医院室外声景观评价影响因素分析——以长沙市中心医院为例

大型综合医院室外本是医患康复疗养、舒缓身心的场所,但并未引起足够的重视,噪声影响严重,声景观较差.该文以长沙市中心医院为例,通过定点实测结合问卷调查的方式,探究影响大型综合医院室外声景观评价结果的因素.结果表明:长沙市中心医院室外声景观整体满意度一般,语义词调查结果整体偏向贬义负值,受访者身份、调查时间和声源构成对声景...     

1980—2018年镇赉县湿地景观格局变化与人为干扰的关系

以吉林省最大湿地保留区镇赉县为研究区,基于1980—2018年8期土地利用数据,采用网格分析法研究湿地景观格局变化规律及景观指数与人为干扰度的关系。结果表明：（1）镇赉县湿地面积减少290.7 km2,水体、滩地、沼泽变化率分别为-0.45,-2.97和-4.84 km²·a^-1。（2）镇赉县湿地率（PLAND）下降6.1%,且从西北部向东南部逐渐递增;斑块数量（NP）与斑块平均面积（AREA_MN）均呈先上升后下降的趋势,东南部湿地景观破碎化加剧,中部破碎化减缓;湿地连通度的空间分布格局为西北向东南递增,斑块结合度指数（COHESION）在中部地区显著增加,在东南部地区缓慢降低。（3）镇赉县湿地人为干扰度逐渐增强、耕地面积的增加和交通网的扩张是镇赉县湿地面积萎缩、景观破碎化加剧和连通度降低的主要人为原因。人为干扰度与NP呈显著正相关,与PLAND、AREA_MN、COHESION均呈负相关。稳定西南部和东北部耕地中湿地斑块,进一步加强中部湿地水体连通性,排查东南部湿地核心区违规建筑,实施分区治理,加强对镇赉县现有湿地的保护,以期实现区域可持续发展。