Single Molecule Force Spectroscopy Reveals Critical Roles of Hydrophobic Core Packing in Determining the Mechanical Stability of Protein GB1

Understanding molecular determinants of protein mechanical stability is important not only for elucidating how elastomeric proteins are designed and functioning in biological systems but also for designing protein building blocks with defined nanomechanical properties for constructing novel biomaterials. GB1 is a small α/β protein and exhibits significant mechanical stability. It is thought that the shear topology of GB1 plays an important role in determining its mechanical stability. Here, we combine single molecule atomic force microscopy and protein engineering techniques to investigate the effect of side chain reduction and hydrophobic core packing on the mechanical stability of GB1. We engineered seven point mutants and carried out mechanical ?-value analysis of the mechanical unfolding of GB1. We found that three mutations, which are across the surfaces of two subdomains that are to be sheared by the applied stretching force, in the hydrophobic core (F30L, Y45L, and F52L) result in significant decrease in mechanical unfolding force of GB1. The mechanical unfolding force of these mutants drop by 50-90 pN compared with wild-type GB1, which unfolds at around 180 pN at a pulling speed of 400 nm/s. These results indicate that hydrophobic core packing plays an important role in determining the mechanical stability of GB1 and suggest that optimizing hydrophobic interactions across the surfaces that are to be sheared will likely be an efficient method to enhance the mechanical stability of GB1 and GB1 homologues.     

基于原子力显微镜的单分子力谱在生物研究中的应用

原子力显微镜被广泛应用于生物研究领域,基于原子力显微镜的单分子力谱可以在单分子、单细胞水平上研究生物分子内和分子间的相互作用。 本文介绍了原子力显微镜单分子力谱在生物分子间相互作用、蛋白质去折叠、细胞表面生物分子、细胞力学性质和基于单分子力谱成像等研究中的最新进展。     

单分子光谱检测法的新进展

自上世纪90年代以来，单分子检测已经取得了巨大的进步。它提供了大量非平衡体系中个体或平衡态脉动体系的信息，而这些信息是无法从传统的统计测量中获得的。本文主要介绍近10年来，单分子光谱检测技术从低温到室温、从非溶液介质到水溶液、从固体到活细胞、从有机染料分子到纳米粒子等方面的进展情况。     

基于原子力显微镜的高分子单分子力学研究

原子力显微镜(AFM)从根本上改变了人们对单个原子和分子的作用和认识方式。单分子力谱是基于原子力显微镜力的测量方法。概速了近年来利用基于原子力显微镜的单分子力谱研究单个高分子分子内及分子闻作用力的进展。     

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.     

Direct Identification of Protein–Protein Interactions by Single‐Molecule Force Spectroscopy

Single‐molecule force spectroscopy based on atomic force microscopy (AFM‐SMFS) has allowed the measurement of the intermolecular forces involved in protein‐protein interactions at the molecular level. While intramolecular interactions are routinely identified directly by the use of polyprotein fingerprinting, there is a lack of a general method to directly identify single‐molecule intermolecular unbinding events. Here, we have developed an internally controlled strategy to measure protein–protein interactions by AFM‐SMFS that allows the direct identification of dissociation force peaks while ensuring single‐molecule conditions. Single‐molecule identification is assured by polyprotein fingerprinting while the intermolecular interaction is reported by a characteristic increase in contour length released after bond rupture. The latter is due to the exposure to force of a third protein that covalently connects the interacting pair. We demonstrate this strategy with a cohesin–dockerin interaction.     

硫酸钠诱导单链聚(N-异丙基丙烯酰胺)相变的单分子力谱研究

聚（N-异丙基丙烯酰胺） （PNIPAM）具有独特的相变行为,已成为人们研究蛋白质折叠等生命过程发生机理的模型体系. 我们利用基于原子力显微镜（AFM）的单分子力谱技术（SMFS）研究了单链PNIPAM在硫酸钠诱导下的相转变过程,并定量化了相变后所形成塌缩结构的稳定性. 通过对单链PNIPAM的单分子力谱实验得知：在相变前,得到单调上升的力曲线,对应着PNIPAM无规线团结构的形变过程;相变后,得到的锯齿型力曲线,对应着PNIPAM塌缩结构在外力诱导下的解折叠过程. 首次从单分子水平观察到在外加盐的作用下,单链PNIPAM低温相转变和高温相转变的差异：相比于低温相转变,高温相转变生成的塌缩结构更加稳定.     

单分子荧光成像研究凝血酶核酸适体的折叠

通过对固定在表面的TMR标记凝血酶核酸适体进行单分子荧光成像, 在单分子水平上研究了凝血酶核酸适体的折叠. 在有K+存在的条件下, 核酸适体分子与K+结合后发生折叠, 形成G四分体结构, 使得TMR靠近富含鸟嘌呤的G四分体, 并与鸟嘌呤发生电子转移, 从而导致TMR荧光强度降低. 根据TMR的单分子荧光强度观察到不同K+浓度下核酸适体在折叠和无规卷曲两种状态下的分布. 结果表明, 可利用电子转移引起的荧光强度变化在单分子水平上研究核酸适体构象变化, 这一新方法的建立是对常用的单分子荧光共振能量转移(FRET)法的重要补充.     

原子力显微镜在蛋白单分子结构与功能研究中的应用

原子力显微镜(AFM)以其超常的信噪比、空间分辨率和灵活的探测环境使得单个蛋白分子能在生理条件下成像,在蛋白单分子结构与功能研究中得到广泛地应用。论文介绍了AFM在分子马达、光合蛋白、分子伴侣等蛋白表面结构表征中的应用;AFM在蛋白单分子表面的粘弹性、电荷分布、分子间相互作用等物理属性研究中的进展;总结了AFM在蛋白分子功能研究和单分子操纵中的应用。     

Single‐Molecule Force Spectroscopy on Carrageenan by Means of AFM

A marked difference in force‐extension curves is observed for carrageenan before and after adding NaI buffer in single‐molecule force spectroscopy by means of atomic force microscopy (AFM). The salt‐induced helix conformation in carrageenan treated with an 0.1 M NaI solution was unfolded under the external force, and a long plateau about 300 pN high could be observed in the force‐extension curves.     

Theoretical Studies of Single Molecule Spectroscopy at Room Temperature

This talk is motivated by recent room-temperature single molecule experiments, which measure the optical spectrum along single molecular trajectories and monitor the molecular dynamics and chemical kinetics of individual reactive systems. These experiments contain new information that requires theoretical models and interpretations. Several aspects of single molecule spectroscopy are analyzed:(1) Event-averaged single molecule quantities are calculated, with the prediction of the echo signal in the joint event probability distribution function^[1]. Similar to the photon echo phenomenon, the single molecule echo signal measures solvent effects on chemical kinetics. (2) The statistics of single molecule blinking events are often correlated to underlying quantum mechanisms. The distribution functions of waiting-time sequences are examined for several quantum processes, including electron transfer, solvent relaxation, laser-induced emission, and single quantum-dot blinking^[2]. (3) Single molecule measurements of heterogeneous diffusion reveal deviations from the Gaussian distribution of Brownian motion. As a quantitative measure, the non-Gaussian indicator decays asymptotically to zero according to 1/t for finite time correlation, but saturates at a plateau value for power-law correlation.     

Spectroscopic Monitoring of Mechanical Forces during Protein Folding by using Molecular Force Probes

Detailed folding pathways of proteins are still largely unknown. Real‐time monitoring of mechanical forces acting in proteins during structural transitions would provide deep insights into these highly complex processes. Here, we propose two molecular force probes that can be incorporated into the protein backbone to gain insight into the magnitude and direction of mechanical forces acting in proteins during natural folding and unfolding through their optical spectroscopic response. In fact, changes in the infrared and Raman spectra are proportional to the mechanical force deforming the force probes, and the relevant bands can be intensified and shifted to a transparent window in the protein spectrum by isotopic substitution. As a result, the proposed molecular force probes can act as “force rulers”, allowing the spectroscopic observation and measurement of mechanical forces acting within the proteins under natural conditions without external perturbation.     

Spectral Versatility of Single Reef Coral Fluorescent Proteins Detected by Spectrally‐Resolved Single Molecule Spectroscopy

We use spectrally‐resolved room temperature single molecule spectroscopy to yield insights into the occurrence and dynamics of spectral forms of single tetramers of DsRed and its variants DsRed2, Fluorescent Timer, DsRed_N42H and AG4. The red‐emitting chromophore in DsRed and all studied variants readily converts into a high quantum efficiency super‐red emitting form. We propose the existence of two super‐red forms of different quantum efficiencies. The observed emission from the green‐emitting chromophore is consistent with bulk spectroscopy. We further observe distinct new spectral forms from each variant, which we attribute to a photoinduced chemical reaction leading to a truncated form of the red‐emitting chromophore analogous to the chromophore in the visible fluorescent protein zFP538. Our results have implications for the accurate interpretation of biological and biochemical processes illuminated by fluorescent proteins as well as for choosing appropriate experimental configurations.     

Detection of Single Molecule on Water Surface by Confocal Fluorescence Microscopy

In the past decade,several research groups have succeeded in observing single molecule in liquid, and more recently at silica surface in the near-field mode as well as at polymer-air interface in far-field mode. Due to the significance of air-water interface in surface chemistry, we prospect that research works on single molecule detection (SMD) of the air-water surface could open a new era in surface photochemistry and photophysics.     

荧光相关光谱及其在单分子检测中的应用进展

单分子检测在生命科学、化学、物理学等领域具有重要的意义。荧光相关光谱是单分子检测的新技术,在生命科学领域有巨大的应用潜力。综述了荧光相关光谱单分子检测的原理、实验技术以及在生物分子相互作用、活细胞、核酸、疾病诊断、高通量筛选以及与毛细管电泳联用等领域的研究,并展望了其发展前景。