scholarly journals Investigating peptide-lipid interactions at single molecule level

2017 ◽  
Author(s):  
◽  
Tina Rezaie Matin
Keyword(s):  
Small Molecules ◽  
Single Molecule ◽  
Physical Interaction ◽  
Complete Understanding ◽  
Single Molecule Level ◽  
Lipid Interactions ◽  
Atomic Force ◽  
Physical Technique ◽  
Different Types ◽  
Model Protein

Despite the utmost importance of protein- lipid interactions in cellular activity, due to technical difficulties, this class of interactions has not been understood mechanistically. Obtaining a more complete understanding of these interactions would, for example, aid the design of more compatible and effective medicine to target specific cells. We developed a physical technique to study such interactions and investigated the interactions between small portions of a model protein with different types of membrane. We were able to detect physical interaction differences between the two at the single-molecule level. This technique is generalizable to study other small molecule-membrane interactions and helps scientists to have a better understanding of the transport of energy, nutrition and waste in and out of the cells. The machine that has been used in our investigations is a mechanical microscope called an AFM (atomic Force Microscope). In addition to making a topographical images, this tool enables us to pick up small molecules in a controlled and precise manner.

scholarly journals Tracking On-Surface Chemistry with Atomic Precision

Synlett ◽  
2017 ◽  
Vol 28 (19) ◽  
pp. 2509-2516 ◽  
Author(s):  
Peter Jacobse ◽  
Marc-Etienne Moret ◽  
Robertus Klein Gebbink ◽  
Ingmar Swart
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Graphene Nanoribbons ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
The Past ◽  
Atomic Force ◽  
Atomic Precision ◽  
Different Types ◽  
Insight Into

The field of on-surface synthesis has seen a tremendous development in the past decade as an exciting new methodology towards atomically well-defined nanostructures. A strong driving force in this respect is its inherent compatibility with scanning probe techniques, which allows one to ‘view’ the reactants and products at the single-molecule level. In this article, we review the ability of noncontact atomic force microscopy to study on-surface chemical reactions with atomic precision. We highlight recent advances in using noncontact atomic force microscopy to obtain mechanistic insight into reactions and focus on the recently elaborated mechanisms in the formation of different types of graphene nanoribbons.

Atomic Force Microscopy (AFM) for Topography and Recognition Imaging at Single Molecule Level

2013 ◽  
pp. 102-112
Author(s):  
Memed Duman ◽  
Andreas Ebner ◽  
Christian Rankl ◽  
Jilin Tang ◽  
Lilia A. Chtcheglova ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Imaging

Atomic Force Microscopy (AFM) for Topography and Recognition Imaging at Single-Molecule Level

2018 ◽  
pp. 1-14
Author(s):  
Memed Duman ◽  
Yoo Jin Oh ◽  
Rong Zhu ◽  
Michael Leitner ◽  
Andreas Ebner ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Imaging

scholarly journals How Microbes Use Force To Control Adhesion

2020 ◽  
Vol 202 (12) ◽  
Author(s):  
Albertus Viljoen ◽  
Johann Mignolet ◽  
Felipe Viela ◽  
Marion Mathelié-Guinlet ◽  
Yves F. Dufrêne
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Flow Chamber ◽  
Microbial Adhesion ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Adhesive Interactions ◽  
And Function ◽  
Mechanisms Of Adhesion

ABSTRACT Microbial adhesion and biofilm formation are usually studied using molecular and cellular biology assays, optical and electron microscopy, or laminar flow chamber experiments. Today, atomic force microscopy (AFM) represents a valuable addition to these approaches, enabling the measurement of forces involved in microbial adhesion at the single-molecule level. In this minireview, we discuss recent discoveries made applying state-of-the-art AFM techniques to microbial specimens in order to understand the strength and dynamics of adhesive interactions. These studies shed new light on the molecular mechanisms of adhesion and demonstrate an intimate relationship between force and function in microbial adhesins.

scholarly journals Broken force dispersal network in tip-links by the mutations at the Ca2+-binding residues induces hearing-loss

2019 ◽  
Vol 476 (16) ◽  
pp. 2411-2425 ◽  
Author(s):  
Jagadish P. Hazra ◽  
Amin Sagar ◽  
Nisha Arora ◽  
Debadutta Deb ◽  
Simerpreet Kaur ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Inner Ear ◽  
Single Molecule ◽  
Force Sensor ◽  
Force Sensors ◽  
Single Molecule Level ◽  
Conformational Variability ◽  
Atomic Force ◽  
Wide Range ◽  
And Function

Abstract Tip-link as force-sensor in hearing conveys the mechanical force originating from sound to ion-channels while maintaining the integrity of the entire sensory assembly in the inner ear. This delicate balance between structure and function of tip-links is regulated by Ca2+-ions present in endolymph. Mutations at the Ca2+-binding sites of tip-links often lead to congenital deafness, sometimes syndromic defects impairing vision along with hearing. Although such mutations are already identified, it is still not clear how the mutants alter the structure-function properties of the force-sensors associated with diseases. With an aim to decipher the differences in force-conveying properties of the force-sensors in molecular details, we identified the conformational variability of mutant and wild-type tip-links at the single-molecule level using FRET at the endolymphatic Ca2+ concentrations and subsequently measured the force-responsive behavior using single-molecule force spectroscopy with an Atomic Force Microscope (AFM). AFM allowed us to mimic the high and wide range of force ramps (103–106 pN s−1) as experienced in the inner ear. We performed in silico network analysis to learn that alterations in the conformations of the mutants interrupt the natural force-propagation paths through the sensors and make the mutant tip-links vulnerable to input forces from sound stimuli. We also demonstrated that a Ca2+ rich environment can restore the force-response of the mutant tip-links which may eventually facilitate the designing of better therapeutic strategies to the hearing loss.

scholarly journals Profound Nanoscale Structural and Biomechanical Changes in DNA Helix upon Treatment with Anthracycline Drugs

2020 ◽  
Vol 21 (11) ◽  
pp. 4142
Author(s):  
Aleksandra Kaczorowska ◽  
Weronika Lamperska ◽  
Kaja Frączkowska ◽  
Jan Masajada ◽  
Sławomir Drobczyński ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Regulatory Elements ◽  
Dna Molecules ◽  
Anthracycline Antibiotics ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Microscopy Analysis ◽  
Dna Regulatory Elements

In our study, we describe the outcomes of the intercalation of different anthracycline antibiotics in double-stranded DNA at the nanoscale and single molecule level. Atomic force microscopy analysis revealed that intercalation results in significant elongation and thinning of dsDNA molecules. Additionally, using optical tweezers, we have shown that intercalation decreases the stiffness of DNA molecules, that results in greater susceptibility of dsDNA to break. Using DNA molecules with different GC/AT ratios, we checked whether anthracycline antibiotics show preference for GC-rich or AT-rich DNA fragments. We found that elongation, decrease in height and decrease in stiffness of dsDNA molecules was highest in GC-rich dsDNA, suggesting the preference of anthracycline antibiotics for GC pairs and GC-rich regions of DNA. This is important because such regions of genomes are enriched in DNA regulatory elements. By using three different anthracycline antibiotics, namely doxorubicin (DOX), epirubicin (EPI) and daunorubicin (DAU), we could compare their detrimental effects on DNA. Despite their analogical structure, anthracyclines differ in their effects on DNA molecules and GC-rich region preference. DOX had the strongest overall effect on the DNA topology, causing the largest elongation and decrease in height. On the other hand, EPI has the lowest preference for GC-rich dsDNA. Moreover, we demonstrated that the nanoscale perturbations in dsDNA topology are reflected by changes in the microscale properties of the cell, as even short exposition to doxorubicin resulted in an increase in nuclei stiffness, which can be due to aberration of the chromatin organization, upon intercalation of doxorubicin molecules.

PRINCIPLES OF SINGLE-MOLECULE MANIPULATION AND ITS APPLICATION IN BIOLOGICAL PHYSICS

2012 ◽  
Vol 26 (13) ◽  
pp. 1230006 ◽  
Author(s):  
WEI-HUNG CHEN ◽  
JONATHAN D. WILSON ◽  
SITHARA S. WIJERATNE ◽  
SARAH A. SOUTHMAYD ◽  
KUAN-JIUH LIN ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Biological Molecules ◽  
Force Detection ◽  
Biomolecular Systems ◽  
Single Molecule Level ◽  
Detection Techniques ◽  
Atomic Force ◽  
Manipulation System ◽  
Single Molecule Manipulation

Recent advances in nanoscale manipulation and piconewton force detection provide a unique tool for studying the mechanical and thermodynamic properties of biological molecules and complexes at the single-molecule level. Detailed equilibrium and dynamics information on proteins and DNA have been revealed by single-molecule manipulation and force detection techniques. The atomic force microscope (AFM) and optical tweezers have been widely used to quantify the intra- and inter-molecular interactions of many complex biomolecular systems. In this article, we describe the background, analysis, and applications of these novel techniques. Experimental procedures that can serve as a guide for setting up a single-molecule manipulation system using the AFM are also presented.

On the way to supramolecular photochemistry at the single-molecule level

2006 ◽  
Vol 78 (12) ◽  
pp. 2247-2259 ◽  
Author(s):  
Christian Schäfer ◽  
Björn Decker ◽  
Matthias Letzel ◽  
Francesca Novara ◽  
Rainer Eckel ◽  
...  
Keyword(s):  
Single Molecule ◽  
Binding Pocket ◽  
Ion Cyclotron Resonance ◽  
Dynamic Force ◽  
Fticr Mass Spectrometry ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Molecular Length ◽  
First Time

Two examples of artificial supramolecular host-guest systems derived from resorc[4]arenes (calix[n]arenes based on resorcinol) and ammonium ions as guests have been studied by atomic force microscopy (AFM). For the first time, real single-molecule events have been determined for this type of supramolecular complexes and off-rates as well as molecular parameters of single-molecule aggregates such as the depths of the binding pocket (molecular length parameter) could be measured by applying the methods of dynamic force spectroscopy. In addition, this technique was also applied to differentiate between the two states (open and closed) of a photoswitchable resorc[4]arene-anthracene tweezer. An investigation of the exchange rates of various complexes in the gas phase by means of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry confirmed the results of the AFM study.

scholarly journals Nonspecific Protein Adsorption at the Single Molecule Level Studied by Atomic Force Microscopy

Langmuir ◽  
2007 ◽  
Vol 23 (20) ◽  
pp. 9921-9923 ◽  
Author(s):  
Peter Schön ◽  
Martin Görlich ◽  
Michiel J. J. Coenen ◽  
Hans A. Heus ◽  
Sylvia Speller
Keyword(s):  
Atomic Force Microscopy ◽  
Protein Adsorption ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Nonspecific Protein Adsorption

scholarly journals Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shintaroh Kubo ◽  
Suguru Kato ◽  
Kazuyuki Nakamura ◽  
Noriyuki Kodera ◽  
Shoji Takada
Keyword(s):  
Atomic Force Microscopy ◽  
Kalman Filter ◽  
Single Molecule ◽  
High Speed ◽  
Ground Truth ◽  
Bayesian Filtering ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Kalman Smoother ◽  
Atomic Force

Abstract High-speed atomic force microscopy (HS-AFM) is a scanning probe microscopy that can capture structural dynamics of biomolecules in real time at single molecule level near physiological condition. Albeit much improvement, while scanning one frame of HS-AFM movies, biomolecules often change their conformations largely. Thus, the obtained frame images can be hampered by the time-difference, the asynchronicity, in the data acquisition. Here, to resolve this data asynchronicity in the HS-AFM movie, we developed Kalman filter and smoother methods, some of the sequential Bayesian filtering approaches. The Kalman filter/smoother methods use alternative steps of a short time-propagation by a linear dynamical system and a correction by the likelihood of AFM data acquired pixel by pixel. We first tested the method using a toy model of a diffusing cone, showing that the Kalman smoother method outperforms to reproduce the ground-truth movie. We then applied the Kalman smoother to a synthetic movie for conformational change dynamics of a motor protein, i.e., dynein, confirming the superiority of the Kalman smoother. Finally, we applied the Kalman smoother to two real HS-AFM movies, FlhAC and centralspindlin, reducing distortion and noise in the AFM movies. The method is general and can be applied to any HS-AFM movies.

Sign in / Sign up

Export Citation Format

Share Document