Predicting the placement of biomolecular structures on AFM substrates based on electrostatic interactions

被引:2
|
作者
Amyot, Romain [1 ]
Nakamoto, Kaho [1 ]
Kodera, Noriyuki [1 ]
Flechsig, Holger [1 ]
机构
[1] Kanazawa Univ, Nano Life Sci Inst WPI NanoLSI, Kanazawa, Ishikawa, Japan
基金
日本科学技术振兴机构;
关键词
AFM (atomic force microscope); sample placement; electrostatic interaction; protein dynamics analysis; image analysis; software application;
D O I
10.3389/fmolb.2023.1264161
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Atomic force microscopy (AFM) and high-speed AFM allow direct observation of biomolecular structures and their functional dynamics. Based on scanning the molecular surface of a sample deposited on a supporting substrate by a probing tip, topographic images of its dynamic shape are obtained. Critical to successful AFM observations is a balance between immobilization of the sample while avoiding too strong perturbations of its functional conformational dynamics. Since the sample placement on the supporting substrate cannot be directly controlled in experiments, the relative orientation is a priori unknown, and, due to limitations in the spatial resolution of images, difficult to infer from a posteriori analysis, thus hampering the interpretation of measurements. We present a method to predict the macromolecular placement of samples based on electrostatic interactions with the AFM substrate and demonstrate applications to HS-AFM observations of the Cas9 endonuclease, an aptamer-protein complex, the Monalysin protein, and the ClpB molecular chaperone. The model also allows predictions of imaging stability taking into account buffer conditions. We implemented the developed method within the freely available BioAFMviewer software package. Predictions based on available structural data can therefore be made even prior to an actual experiment, and the method can be applied for post-experimental analysis of AFM imaging data.
引用
收藏
页数:13
相关论文
共 50 条
  • [1] Electrostatic interactions in biomolecular systems
    Hünenberger, PH
    Börjesson, U
    Lins, RD
    CHIMIA, 2001, 55 (10) : 861 - 866
  • [2] ON THE TREATMENT OF ELECTROSTATIC INTERACTIONS IN BIOMOLECULAR SIMULATION
    STOTE, RH
    STATES, DJ
    KARPLUS, M
    JOURNAL DE CHIMIE PHYSIQUE ET DE PHYSICO-CHIMIE BIOLOGIQUE, 1991, 88 (11-12) : 2419 - 2433
  • [3] AI accurately predicting the structure of biomolecular interactions
    Peng, Zhenling
    Lu, Peilong
    Yang, Jianyi
    CELL RESEARCH, 2024, 34 (09) : 601 - 602
  • [4] On the treatment of long-range electrostatic interactions in biomolecular simulations
    Yonetani, Yoshiteru
    Frontiers of Computational Science, 2007, : 209 - 214
  • [5] BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics
    Amyot, Romain
    Flechsig, Holger
    PLOS COMPUTATIONAL BIOLOGY, 2020, 16 (11)
  • [6] Order N algorithm for computation of electrostatic interactions in biomolecular systems
    Lu, Benzhuo
    Cheng, Xiaolin
    Huang, Jingfang
    McCammon, J. Andrew
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (51) : 19314 - 19319
  • [7] Accelerating computations to order N for electrostatic interactions of biomolecular systems
    Lu, Benzhuo
    Cheng, Xiaolin
    Huang, Jingfang
    McCammon, J. Andrew
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2006, 232 : 206 - 206
  • [8] Hierarchical biomolecular self-assembly through electrostatic interactions.
    Wong, GCL
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2004, 227 : U804 - U804
  • [9] Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution
    Hassan, Sergio A.
    JOURNAL OF PHYSICAL CHEMISTRY B, 2007, 111 (01): : 227 - 241
  • [10] ELECTROSTATIC INTERACTIONS AND SECONDARY STRUCTURES IN PROTEINS
    JERNIGAN, RL
    MIYAZAWA, S
    SZU, SC
    BIOPHYSICAL JOURNAL, 1980, 32 (01) : 93 - 95