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.     

东海区海岸带景观格局变化对生态系统服务价值的影响

对大尺度、长时序的海岸带景观格局和生态系统服务价值(ecosystem services value,ESV)的研究，有利于更好地促进区域生态系统保护工作的开展。以1990，1995，2000，2005，2010，2015年6期遥感影像解译结果为基础，对东海区海岸带景观格局变化特征和ESV时空演变进行了分析，并探讨了ESV与景观格局变化二者间的关系。结果表明，1990—2015年的25 a间，受人类活动的影响，东海区海岸带农田和海域面积大量减少，建设用地面积大幅增加；在所研究的5类地貌类型中，除中起伏山地外，其余地貌类型景观面积转移都较为剧烈。25 a间东海区海岸带斑块数量、斑块密度、边界密度、shannon多样性指数等不断增加，景观破碎化、复杂化、多样化增强。农田景观的最大斑块指数、形态指数、边界密度等变化均较大。东海区海岸带ESV呈先增加后减小的趋势，其中森林景观对ESV总量贡献最大；水文调节、生物多样性维持、气候调节、土壤保持、废物处理和气体调节是东海区海岸带主要的生态系统服务功能；在空间上表现出以单位面积中、低ESV为主导的空间分布，高、极高和极低ESV分布较少。研究区ESV总量与农田和海域以及水域和建设用地面积显著相关；与斑块密度、边界密度和形态指数呈显著负相关。同时，食物生产、气体调节、气候调节、土壤保持和生物多样性维持的服务价值与景观指数间均显著相关。