Toward Measuring In-Vitro Single Molecule Force Fields Using a Scanning Force Microscope

2000 ◽  
Vol 6 (S2) ◽  
pp. 970-971
Author(s):  
S. J. Eppell ◽  
B. A. Todd ◽  
F. R. Zypman
Keyword(s):  
Single Molecule ◽  
Electrostatic Interactions ◽  
Force Fields ◽  
Three Dimensional ◽  
Surface Force ◽  
Scanning Force Microscopy ◽  
Near Surface ◽  
Scanning Force ◽  
State Of Affairs

The interaction of surfaces with their surroundings can be described as arising from force fields generated by molecules at the surface of interest. This statement is true for electrostatic interactions of proteins on cell membranes as well as steric interactions of macromolecules on polymer surfaces. To better understand these systems and ultimately to design superior materials, it is necessary to make direct measurements of these near-surface molecular scale force fields. Scanning force microscopy (SFM) holds some promise in the endeavor to make surface force measurements in a full three dimensional submolecularly resolved space. In-vitro measurements present a problem in that the force fields tend to be very short ranged. This necessitates placing the SFM probe very near the surface in order to measure the fields. The ubiquitous van der Waals attraction tends to induce an instability in the SFM instrument under these conditions leading to a non-equilibrium state. We have carefully examined this state of affairs and found that it is essential to use a substantially more sophisticated method to analyze SFM data than is commonly performed.

scholarly journals Tip dependence of three-dimensional scanning force microscopy images of calcite–water interfaces investigated by simulation and experiments

Nanoscale ◽  
2020 ◽  
Vol 12 (24) ◽  
pp. 12856-12868 ◽  
Author(s):  
Keisuke Miyazawa ◽  
John Tracey ◽  
Bernhard Reischl ◽  
Peter Spijker ◽  
Adam S. Foster ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Scanning Force Microscopy ◽  
Force Microscopy ◽  
Scanning Force ◽  
Microscopy Images

In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite–water interfaces by experiments and simulations.

scholarly journals The extruded non-template strand determines the architecture of R-loops

2019 ◽  
Vol 47 (13) ◽  
pp. 6783-6795 ◽  
Author(s):  
Yeraldinne Carrasco-Salas ◽  
Amélie Malapert ◽  
Shaheen Sulthana ◽  
Bastien Molcrette ◽  
Léa Chazot-Franguiadakis ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Stability ◽  
Three Dimensional ◽  
Dna Breaks ◽  
Yeast Gene ◽  
Physical Constraints ◽  
Force Microscopy ◽  
Template Strand ◽  
Atomic Force

Abstract Three-stranded R-loop structures have been associated with genomic instability phenotypes. What underlies their wide-ranging effects on genome stability remains poorly understood. Here we combined biochemical and atomic force microscopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the model Airn locus in vitro adopt a defined set of three-dimensional conformations characterized by distinct shapes and volumes, which we call R-loop objects. Interestingly, we show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks.

scholarly journals Structure, Surface Interactions, and Compressibility of Bacterial S-Layers through Scanning Force Microscopy and the Surface Force Apparatus

2006 ◽  
Vol 90 (5) ◽  
pp. 1821-1829 ◽  
Author(s):  
Alberto Martín-Molina ◽  
Susana Moreno-Flores ◽  
Eric Perez ◽  
Dietmar Pum ◽  
Uwe B. Sleytr ◽  
...  
Keyword(s):  
Surface Force ◽  
Scanning Force Microscopy ◽  
Surface Interactions ◽  
Surface Force Apparatus ◽  
Force Microscopy ◽  
Structure Surface ◽  
Scanning Force

Unfolding single RNA molecules: bridging the gap between equilibrium and non-equilibrium statistical thermodynamics

2005 ◽  
Vol 38 (4) ◽  
pp. 291-301 ◽  
Author(s):  
Carlos Bustamante
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Biological Systems ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Fluctuation Theorems ◽  
Rna Molecules ◽  
The Times ◽  
Non Equilibrium

During the last 15 years, scientists have developed methods that permit the direct mechanical manipulation of individual molecules. Using this approach, they have begun to investigate the effect of force and torque in chemical and biochemical reactions. These studies span from the study of the mechanical properties of macromolecules, to the characterization of molecular motors, to the mechanical unfolding of individual proteins and RNA. Here I present a review of some of our most recent results using mechanical force to unfold individual molecules of RNA. These studies make it possible to follow in real time the trajectory of each molecule as it unfolds and characterize the various intermediates of the reaction. Moreover, if the process takes place reversibly it is possible to extract both kinetic and thermodynamic information from these experiments at the same time that we characterize the forces that maintain the three-dimensional structure of the molecule in solution. These studies bring us closer to the biological unfolding processes in the cell as they simulate in vitro, the mechanical unfolding of RNAs carried out in the cell by helicases. If the unfolding process occurs irreversibly, I show here that single-molecule experiments can still provide equilibrium, thermodynamic information from non-equilibrium data by using recently discovered fluctuation theorems. Such theorems represent a bridge between equilibrium and non-equilibrium statistical mechanics. In fact, first derived in 1997, the first experimental demonstration of the validity of fluctuation theorems was obtained by unfolding mechanically a single molecule of RNA. It is perhaps a sign of the times that important physical results are these days used to extract information about biological systems and that biological systems are being used to test and confirm fundamental new laws in physics.

scholarly journals Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction

2012 ◽  
Vol 3 ◽  
pp. 637-650 ◽  
Author(s):  
Mehmet Z Baykara ◽  
Omur E Dagdeviren ◽  
Todd C Schwendemann ◽  
Harry Mönig ◽  
Eric I Altman ◽  
...  
Keyword(s):  
Force Fields ◽  
Image Interpretation ◽  
Three Dimensional ◽  
Surface Force ◽  
Interaction Force ◽  
Atomic Scale ◽  
Atomic Resolution ◽  
Spatial Dimensions ◽  
Scale Properties ◽  
Measurement Strategies

Noncontact atomic force microscopy (NC-AFM) is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation. In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface.

Scanning Force Microscopy of the Interaction Events between a Single Molecule of Heavy Meromyosin and Actin

1997 ◽  
Vol 234 (1) ◽  
pp. 178-182 ◽  
Author(s):  
Hideo Nakajima ◽  
Yuki Kunioka ◽  
Katsushi Nakano ◽  
Kohtaro Shimizu ◽  
Masaru Seto ◽  
...  
Keyword(s):  
Single Molecule ◽  
Scanning Force Microscopy ◽  
Heavy Meromyosin ◽  
Force Microscopy ◽  
Scanning Force

scholarly journals Criteria for Engineering Cutinases: Bioinformatics Analysis of Catalophores

Catalysts ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 784
Author(s):  
Sara Fortuna ◽  
Marco Cespugli ◽  
Anamaria Todea ◽  
Alessandro Pellis ◽  
Lucia Gardossi
Keyword(s):  
Electrostatic Interactions ◽  
Catalytic Properties ◽  
Three Dimensional ◽  
Structural Features ◽  
Fungal Enzymes ◽  
Rational Engineering ◽  
Molecular Interaction Fields ◽  
Bioinformatics Study ◽  
Chain Lengths

Cutinases are bacterial and fungal enzymes that catalyze the hydrolysis of natural cutin, a three-dimensional inter-esterified polyester with epoxy-hydroxy fatty acids with chain lengths between 16 and 18 carbon atoms. Due to their ability to accept long chain substrates, cutinases are also effective in catalyzing in vitro both the degradation and synthesis of several synthetic polyesters and polyamides. Here, we present a bioinformatics study that intends to correlate the structural features of cutinases with their catalytic properties to provide rational basis for their effective exploitation, particularly in polymer synthesis and biodegradation. The bioinformatics study used the BioGPS method (Global Positioning System in Biological Space) that computed molecular descriptors based on Molecular Interaction Fields (MIFs) described in the GRID force field. The information was used to generate catalophores, spatial representations of the ability of each enzymatic active site to establish hydrophobic and electrostatic interactions. These tools were exploited for comparing cutinases to other serine-hydrolases enzymes, namely lipases, esterases, amidases and proteases, and for highlighting differences and similarities that might guide rational engineering strategies. Structural features of cutinases with their catalytic properties were correlated. The “catalophore” of cutinases indicate shared features with lipases and esterases.

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