BMB November 17, Single Molecule Biophysics (I)
|
|
- Pierce Burns
- 5 years ago
- Views:
Transcription
1 BMB November 17, Single Molecule Biophysics (I)
2 Goals 1. Understand the information SM experiments can provide 2. Be acquainted with different SM approaches 3. Learn to interpret SM results
3 Text books Methods in Molecular Biophysics - chapter F4 Single molecule detection - chapter F5 single molecule manipulation Useful Readings - Joo et al., Annu. Rev. Biochem 77: 51 (2008) Advances in single-molecule fluorescence methods - Cecconi et al., Proc. Int. School Enrico Fermi, Societa Italiana di Fisica: 145 (2007) Studying protein folding with laser tweezers - Engel & Gaub, Annu. Rev. Biochem 77: 127 (2008) Structure and Mechanics of membrane proteins
4 Why Single Molecules? 1. Overcome Sample Heterogeneity
5 Why Single Molecules? 2. Observe intermediates that do not accumulate G
6 Why Single Molecules? 3. Dissect Multiple Pathways Molecules reaction
7 Why Single Molecules? 4. Overcome Loss of molecular synchrony Molecules
8 Challenges in Single Molecules Studies 1. Establish conditions so that a single molecule is detected 2. Sensitivity - signal from a single molecule must be detected above background
9 Earliest Single Molecule Studies: Patch Clamp A glass pipette makes contact with a small area of membrane containing a single channel Mild suction creates a tight seal with membrane allows control of membrane potential to study the voltage dependence of the channel Bert Sakmann & Erwin Neher, 1981
10 Different Patch Clamp Configurations
11 Single Channel Studies of AchR QX-222 open QX222 +QX222 closed Charnet et al, Neuron 2: 87 (1990)
12 Characterize the kinetics of channel opening p i = Ae (t t 0 )/τ τ = 1/F dwell time, blocked Charnet et al, Neuron 2: 87 (1990)
13 Pushing the limit of Patch Clamp Techniques Reduce stray capacitance of micropipettes thick wall, hard borosilicate or quartz faster detectors with reduced noise => <3 µs time resolution membranes with higher resistance reconstituted liposomes and vesicles instead of spheroplast
14 Detecting channel substates at µs resolution MscS channel recording at 3 µs resolution open 2/3 open Kinetic analysis closed Voltage-gating response equilibrium analysis Shapovalov & Lester, J. Gen. Physiol. 124: 151 (2004)
15 New Advances in Single Molecule Techniques Atomic Force Microscopy Single Molecule Manipulation - optical traps and tweezers Single Molecule Fluorescence Single Molecule Imaging (STORM, PALM)
16 Atomic Force Microscopy Deflections resulting from tip-sample forces are detected: - van der Waals - capillary - electrostatic - magnetic - solvation Feed-back mechanism adjusts tip-to-sample distance to maintain a constant force
17 Tips in AFM The ideal AFM tip has a small R c and Φ 0. Mostly carbon nanonubules
18 Imaging Modes in AFM Static Mode: tip deflection is the feedback signal - very high resolution - Lateral shearing forces pushes sample off - Needs low stiffness cantilevers
19 Imaging Modes in AFM Dynamic Mode: cantilever is externally oscillated - changes in oscillation amplitude, phase or frequency due to tip-sample interactions provide the feedback signal - stiff cantilevers provide stability close to the surface - minimizes damage and displacement of the sample
20 AFM Images Single molecules of poly(2-vinylpyridine) recorded by tapping mode AFM Roiter & Minko, JACS 127: (2005)
21 AFM allows Proteins to be Imaged in Native Membrane Bacterhodopsin trimer on purple membrane Low force High force Muller et al, Biochim. Biophys. Acta 1460: 27 (2000)
22 Probe conformational dynamics of membrane proteins with ultrafast AFM Lipid bilayers containing SecYEG channel Gary et al, PNAS 2013: 16868
23 Probe conformational dynamics of membrane proteins with fast AFM Gary et al, PNAS 2013: 16868
24 New Advances in Single Molecule Techniques Atomic Force Microscopy Single Molecule Manipulation - optical traps and tweezers Single Molecule Fluorescence
25 Single Molecule Manipulations AFM can be used to mechanically manipulate single molecules and study unfolding; However, force constants are nn/nm with RMS force noise of 1 15 pn. Suited to monitor events under high force. Low force lazer tweezers: RMS noise < 1 pn. Allow studies of molecular events occurring under low forces. Examples: - protein / RNA folding / unfolding - molecular motors - transcription / translation
26 Principle of Optical tweezers Attracts dielectric particles in a highly focused laser beam. Strong electric field gradient across beam waist.
27 Principle of Optical tweezers Balance between momentum from reflected and refracted rays traps bead downstream of the light focus.
28 Dual-beam Optical Trap Scattering forces by reflected rays are canceled; Bead is trapped at the light focus.
29 Light-momentum Force Sensor Offset distance measured by PSD is converted into momentum flux of the tapping beam W - light intensity; F = (W/c) ( x/r L ) R L - focal length of the lens bead position is proportional to applied force for displacement up to ~200 nm => measures both displacement and force
30 Basic Optical Tweezer Setup
31 Different Geometries of Optical Tweezers DNA/RNA/protein folding motors
32 RNase H Folding: Bulk studies An intermediate (I) forms within the instrument deadtime (<12 ms) protected from H/D exchange in I Questions: - Is I a distinct state, or a redistribution of the unfolded protein? - Is I on or off the pathway? - Is formation of I obligatory for RNase H folding?
33 Single Molecule Study: RNase H Folding Experimental setup Cecconi et al, Science 309: 2057 (2005)
34 DNA handles do not affect RNase H s Global Structure Folding Enzymatic activity Cecconi et al, Science 309: 2057 (2005)
35 Force-Extension Curves for Individual RNase H Molecules Unfolds in a two-state manner (N U) at ~ 19 pn Refolding occurs through an intermediate (I) at ~ 5.5 pn I further refolds to N at lower foces Cecconi et al, Science 309: 2057 (2005)
36 Force-Extension Curves for Individual RNase H Molecules Unfolds in a two-state manner (N U) at ~ 19 pn Refolding occurs through an intermediate (I) at ~ 5.5 pn I further refolds to N at lower foces I can be further unfolded in the next cycle at ~5.5 pn Cecconi et al, Science 309: 2057 (2005)
37 Direct Observation of Reversible Folding / Unfolding of I at low pulling speed Molecules hop between I and U states at forces close to 5.5 pn Cecconi et al, Science 309: 2057 (2005)
38 I directly Folds into the Native State I is an obligatory intermediate during folding Cecconi et al, Science 309: 2057 (2005)
39 Equilibrium analysis of I U transition I U distance unfolding free energy at F = 0 x = 11 ± 2 nm G = 4 ± 1 kcal/mol; agrees with bulk studies (3.6 kcal/mol) Cecconi et al, Science 309: 2057 (2005)
40 Analysis of the kinetics of I unfolding k I U = 9.1 s -1 k U I = 3.3 s -1 Instrument contribution I distance x I U = 5 ± 1 nm x U I = 6 ± 2 nm unfolding rate at F = 0 I is a pliable structure that can deform substantially Cecconi et al, Science 309: 2057 (2005)
41 Free Energy Landscape of RNase H Cecconi et al, Science 309: 2057 (2005)
42 DNA Packaging Motor in phage Φ29 Three layers: gp10: dodecamer (seal) Prohead-RNA: pentamer (o-ring) gp16: pentamer (motor) Prohead-RNA gp10: connector
43 Study DNA packaging by Φ29 motor with optical trap Smith et al, Nature 413:478 (2001)
44 Follow the dynamics of DNA packaging: Constant Feedback Mode Smith et al, Nature 413:478 (2001)
45 Highly efficient DNA packaging by Φ29 motor > 5 µm DNA can be packaged by a single motor highly processive motor takes ~5.5 min to package the entire Φ29 genome Smith et al, Nature 413:478 (2001)
46 DNA packaging against internal pressure Packaging slows down when the genome is > 50% filled Rate decrease results from internal pressure buildup in the prohead Smith et al, Nature 413:478 (2001)
47 Measure force during packaging: No-feedback Mode Smith et al, Nature 413:478 (2001)
48 Motor can work against 57 pn external force The most powerful motor studied to date Smith et al, Nature 413:478 (2001)
49 Internal pressure builds up as the genome is packaged Internal force reaches 50 pn when the whole genome is packaged can be used to initiate DNA injection during infection Smith et al, Nature 413:478 (2001)
50 Pauses and Slips during packaging Pauses: ATP binding? Slips: dissociation and re-binding Smith et al, Nature 413:478 (2001)
51 Dual beam laser traps allow more sensitive detection Moffitt et al, Nature 457:446 (2009)
52 Observation of discrete steps with ATP-dependent pauses pause mean step size ~ 10 bp pauses: ATP-binding bursts: power stroke burst Moffitt et al, Nature 457:446 (2009)
Experimental biophysics: Optical tweezer lab Supervisor: Stefan Holm,
Experimental biophysics: Optical tweezer lab :, stefan.holm@ftf.lth.se Written by Jason Beech & Henrik Persson, March 2009. Modified 2014 Karl Adolfsson, 2016 Experimental Biophysics: FAF010F, FYST23,
More informationTecniche sperimentali: le optical tweezers
Tecniche sperimentali: le optical tweezers Le tecniche di molecola singola rispetto a quelle di insieme ensemble z z z z z z frequency activity activity time z z z Single molecule frequency activity activity
More informationBMB Class 17, November 30, Single Molecule Biophysics (II)
BMB 178 2018 Class 17, November 30, 2018 15. Single Molecule Biophysics (II) New Advances in Single Molecule Techniques Atomic Force Microscopy Single Molecule Manipulation - optical traps and tweezers
More informationScanning Force Microscopy
Scanning Force Microscopy Roland Bennewitz Rutherford Physics Building 405 Phone 398-3058 roland.bennewitz@mcgill.ca Scanning Probe is moved along scan lines over a sample surface 1 Force Microscopy Data
More informationMeasurements of interaction forces in (biological) model systems
Measurements of interaction forces in (biological) model systems Marina Ruths Department of Chemistry, UMass Lowell What can force measurements tell us about a system? Depending on the technique, we might
More informationAnatoly B. Kolomeisky. Department of Chemistry CAN WE UNDERSTAND THE COMPLEX DYNAMICS OF MOTOR PROTEINS USING SIMPLE STOCHASTIC MODELS?
Anatoly B. Kolomeisky Department of Chemistry CAN WE UNDERSTAND THE COMPLEX DYNAMICS OF MOTOR PROTEINS USING SIMPLE STOCHASTIC MODELS? Motor Proteins Enzymes that convert the chemical energy into mechanical
More informationOptical Tweezers -working principles and applications
Optical Tweezers -working principles and applications Photo taken from the WWW Star Trek Picture Page Biophysics with optical tweezers Optical tweezers use forces of laser radiation pressure to trap small
More information3.052 Nanomechanics of Materials and Biomaterials Thursday 02/08/06 Prof. C. Ortiz, MIT-DMSE I LECTURE 2 : THE FORCE TRANSDUCER
I LECTURE 2 : THE FORCE TRANSDUCER Outline : LAST TIME : WHAT IS NANOMECHANICS... 2 HOW CAN WE MEASURE SUCH TINY FORCES?... 3 EXAMPLE OF A FORCE TRANSDUCER... 4 Microfabricated cantilever beams with nanosized
More informationPinze ottiche. Ciro Cecconi Dipartimento di Fisica, Informatica e Matematica Università degli Studi di Modena and Reggio Emilia
Pinze ottiche Ciro Cecconi Dipartimento di Fisica, Informatica e Matematica Università degli Studi di Modena and Reggio Emilia UNIVERSITA DEGLI STUDI di Modena e Reggio Emilia E-mail: ciro.cecconi@unimore.it
More informationScanning Tunneling Microscopy
Scanning Tunneling Microscopy References: 1. G. Binnig, H. Rohrer, C. Gerber, and Weibel, Phys. Rev. Lett. 49, 57 (1982); and ibid 50, 120 (1983). 2. J. Chen, Introduction to Scanning Tunneling Microscopy,
More informationAtomic and molecular interactions. Scanning probe microscopy.
Atomic and molecular interactions. Scanning probe microscopy. Balázs Kiss Nanobiotechnology and Single Molecule Research Group, Department of Biophysics and Radiation Biology 27. November 2013. 2 Atomic
More informationAtomic Force Microscopy imaging and beyond
Atomic Force Microscopy imaging and beyond Arif Mumtaz Magnetism and Magnetic Materials Group Department of Physics, QAU Coworkers: Prof. Dr. S.K.Hasanain M. Tariq Khan Alam Imaging and beyond Scanning
More informationOptical Tweezers. BGGN 266, Biophysics Lab. June, Trygve Bakken & Adam Koerner
Optical Tweezers BGGN 266, Biophysics Lab June, 2009 Trygve Bakken & Adam Koerner Background There are a wide variety of force spectroscopy techniques available to investigators of biological systems.
More informationOptical Tweezers. The Useful Micro-Manipulation Tool in Research
Optical Tweezers The Useful Micro-Manipulation Tool in Research Student: Nikki Barron Class: Modern Physics/ Biophysics laboratory Advisor: Grant Allen Instructor: David Kleinfeld Date: June 15, 2012 Introduction
More informationSupplementary Figure 1 a) Scheme of microfluidic device fabrication by photo and soft lithography,
a b 1 mm Supplementary Figure 1 a) Scheme of microfluidic device fabrication by photo and soft lithography, (a1, a2) 50nm Pd evaporated on Si wafer with 100 nm Si 2 insulating layer and 5nm Cr as an adhesion
More informationSECOND PUBLIC EXAMINATION. Honour School of Physics Part C: 4 Year Course. Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS
2757 SECOND PUBLIC EXAMINATION Honour School of Physics Part C: 4 Year Course Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS TRINITY TERM 2013 Monday, 17 June, 2.30 pm 5.45 pm 15
More informationOptical Tweezers for Scanning Probe Microscopy
Optical Tweezers for Scanning Probe Microscopy Dr P H Jones Department of Physics and Astronomy UCL www.ucl.ac.uk/~ucapphj CoMPLEx ITPL course MSc Nanotechnology 07 October 2014 Contents 0. Introduction
More information(Entropic) Stochastic Resonance in Biological Systems at Mesoscale
(Entropic) Stochastic Resonance in Biological Systems at Mesoscale Wokyung Sung Department of Physics, POSTECH, IBS center for Self-assembly and Complexity, Pohang, 790-784, South Korea As interconnected,
More informationSECOND PUBLIC EXAMINATION. Honour School of Physics Part C: 4 Year Course. Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS
2757 SECOND PUBLIC EXAMINATION Honour School of Physics Part C: 4 Year Course Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS TRINITY TERM 2011 Monday, 27 June, 9.30 am 12.30 pm Answer
More informationMagnetic Torque Tweezers: measuring torsional stiffness in DNA and RecA DNA filaments
Magnetic Torque Tweezers: measuring torsional stiffness in DNA and RecA DNA filaments Lipfert, J., Kerssemakers, J. W., Jager, T. & Dekker, N. H. Magnetic torque tweezers: measuring torsional stiffness
More informationElasticity of the human red blood cell skeleton
Biorheology 40 (2003) 247 251 247 IOS Press Elasticity of the human red blood cell skeleton G. Lenormand, S. Hénon, A. Richert, J. Siméon and F. Gallet Laboratoire de Biorhéologie et d Hydrodynamique Physico-Chimique,
More informationCharacterization of MEMS Devices
MEMS: Characterization Characterization of MEMS Devices Prasanna S. Gandhi Assistant Professor, Department of Mechanical Engineering, Indian Institute of Technology, Bombay, Recap Characterization of MEMS
More informationOptical Tweezers for Scanning Probe Microscopy
Optical Tweezers for Scanning Probe Microscopy Dr P H Jones Department of Physics and Astronomy UCL www.ucl.ac.uk/~ucapphj CoMPLEx ITPL course MSc Nanotechnology 09 October 2012 Contents 0. Introduction
More informationNitride HFETs applications: Conductance DLTS
Nitride HFETs applications: Conductance DLTS The capacitance DLTS cannot be used for device trap profiling as the capacitance for the gate will be very small Conductance DLTS is similar to capacitance
More informationFree energy recovery in single molecule experiments
Supplementary Material Free energy recovery in single molecule experiments Single molecule force measurements (experimental setup shown in Fig. S1) can be used to determine free-energy differences between
More informationContents. What is AFM? History Basic principles and devices Operating modes Application areas Advantages and disadvantages
Contents What is AFM? History Basic principles and devices Operating modes Application areas Advantages and disadvantages Figure1: 2004 Seth Copen Goldstein What is AFM? A type of Scanning Probe Microscopy
More informationMechanical Proteins. Stretching imunoglobulin and fibronectin. domains of the muscle protein titin. Adhesion Proteins of the Immune System
Mechanical Proteins F C D B A domains of the muscle protein titin E Stretching imunoglobulin and fibronectin G NIH Resource for Macromolecular Modeling and Bioinformatics Theoretical Biophysics Group,
More informationNIS: what can it be used for?
AFM @ NIS: what can it be used for? Chiara Manfredotti 011 670 8382/8388/7879 chiara.manfredotti@to.infn.it Skype: khiaram 1 AFM: block scheme In an Atomic Force Microscope (AFM) a micrometric tip attached
More informationSingle-Molecule Methods I - in vitro
Single-Molecule Methods I - in vitro Bo Huang Macromolecules 2014.03.10 F 1 -ATPase: a case study Membrane ADP ATP Rotation of the axle when hydrolyzing ATP Kinosita group, 1997-2005 Single Molecule Methods
More informationLecture 4 Scanning Probe Microscopy (SPM)
Lecture 4 Scanning Probe Microscopy (SPM) General components of SPM; Tip --- the probe; Cantilever --- the indicator of the tip; Tip-sample interaction --- the feedback system; Scanner --- piezoelectric
More informationModule 26: Atomic Force Microscopy. Lecture 40: Atomic Force Microscopy 3: Additional Modes of AFM
Module 26: Atomic Force Microscopy Lecture 40: Atomic Force Microscopy 3: Additional Modes of AFM 1 The AFM apart from generating the information about the topography of the sample features can be used
More informationCytoskeleton dynamics simulation of the red blood cell
1 Cytoskeleton dynamics simulation of the red blood cell Ju Li Collaborators: Subra Suresh, Ming Dao, George Lykotrafitis, Chwee-Teck Lim Optical tweezers stretching of healthy human red blood cell 2 Malaria
More informationQuantitative Electrophysiology
ECE 795: Quantitative Electrophysiology Notes for Lecture #1 Tuesday, September 18, 2012 1. INTRODUCTION TO EXCITABLE CELLS Historical perspective: Bioelectricity first discovered by Luigi Galvani in 1780s
More informationBasic Laboratory. Materials Science and Engineering. Atomic Force Microscopy (AFM)
Basic Laboratory Materials Science and Engineering Atomic Force Microscopy (AFM) M108 Stand: 20.10.2015 Aim: Presentation of an application of the AFM for studying surface morphology. Inhalt 1.Introduction...
More informationTopological insulator particles as optically induced oscillators: Towards dynamical force measurements and optical rheology
Topological insulator particles as optically induced oscillators: Towards dynamical force measurements and optical rheology Warlley Hudson Campos warlley.campos@ufv.br Departamento de Física - Universidade
More informationStructural investigation of single biomolecules
Structural investigation of single biomolecules NMR spectroscopy and X-ray crystallography are currently the most common techniques capable of determining the structures of biological macromolecules like
More informationChapter 2 Correlation Force Spectroscopy
Chapter 2 Correlation Force Spectroscopy Correlation Force Spectroscopy: Rationale In principle, the main advantage of correlation force spectroscopy (CFS) over onecantilever atomic force microscopy (AFM)
More informationBiophysik der Moleküle!
Biophysik der Moleküle!!"#$%&'()*+,-$./0()'$12$34!4! Molecular Motors:! - linear motors" 6. Dec. 2010! Muscle Motors and Cargo Transporting Motors! There are striking structural similarities but functional
More informationQuantitative Electrophysiology
ECE 795: Quantitative Electrophysiology Notes for Lecture #1 Wednesday, September 13, 2006 1. INTRODUCTION TO EXCITABLE CELLS Historical perspective: Bioelectricity first discovered by Luigi Galvani in
More informationMorphology-dependent resonance induced by two-photon excitation in a micro-sphere trapped by a femtosecond pulsed laser
Morphology-dependent resonance induced by two-photon excitation in a micro-sphere trapped by a femtosecond pulsed laser Dru Morrish, Xiaosong Gan and Min Gu Centre for Micro-Photonics, School of Biophysical
More informationLecture 12: Biomaterials Characterization in Aqueous Environments
3.051J/20.340J 1 Lecture 12: Biomaterials Characterization in Aqueous Environments High vacuum techniques are important tools for characterizing surface composition, but do not yield information on surface
More informationGeneral concept and defining characteristics of AFM. Dina Kudasheva Advisor: Prof. Mary K. Cowman
General concept and defining characteristics of AFM Dina Kudasheva Advisor: Prof. Mary K. Cowman Overview Introduction History of the SPM invention Technical Capabilities Principles of operation Examples
More informationActo-myosin: from muscles to single molecules. Justin Molloy MRC National Institute for Medical Research LONDON
Acto-myosin: from muscles to single molecules. Justin Molloy MRC National Institute for Medical Research LONDON Energy in Biological systems: 1 Photon = 400 pn.nm 1 ATP = 100 pn.nm 1 Ion moving across
More informationarxiv:cond-mat/ v1 [cond-mat.soft] 15 Sep 2006
TOPICAL REVIEW arxiv:cond-mat/0609378v1 [cond-mat.soft] 15 Sep 2006 Single-molecule experiments in biological physics: methods and applications. F. Ritort Departament de Física Fonamental, Facultat de
More informationAnnouncements & Lecture Points
Announcements & Lecture Points Homework 3 (Klaus Schulten s Lecture): Due Wednesday. Quiz returned, next homework on Wednesday. Today s Lecture: Protein Folding, Misfolding, Aggregation. Experimental Approach
More informationLaser Tweezers and Other Advanced Physical Methods
Phys 6715 - Biomedical Physics Laser Tweezers and Other Advanced Physical Methods Yong-qing Li, PhD Department of Physics, East Carolina University Greenville, NC 27858, USA Email: liy@ecu.edu 1 Optical
More informationNIH Public Access Author Manuscript J Phys Condens Matter. Author manuscript; available in PMC 2014 November 20.
NIH Public Access Author Manuscript Published in final edited form as: J Phys Condens Matter. 2013 November 20; 25(46):. doi:10.1088/0953-8984/25/46/463101. Motor Proteins and Molecular Motors: How to
More informationChallenges of Single Ion-Channel Biosensors
Vanderbilt Institute for Integrative Biosystems Research and Education Instrumenting and Control the Single Cell Challenges of Single Ion-Channel Biosensors Fredrick Sachs (SUNY Buffalo) John P. Wikswo
More informationThe Molecular Dynamics Method
The Molecular Dynamics Method Thermal motion of a lipid bilayer Water permeation through channels Selective sugar transport Potential Energy (hyper)surface What is Force? Energy U(x) F = d dx U(x) Conformation
More informationLecture 7 : Molecular Motors. Dr Eileen Nugent
Lecture 7 : Molecular Motors Dr Eileen Nugent Molecular Motors Energy Sources: Protonmotive Force, ATP Single Molecule Biophysical Techniques : Optical Tweezers, Atomic Force Microscopy, Single Molecule
More informationOptical Tweezers as an Application of Electrodynamics
Optical Tweezers as an Application of Electrodynamics Edda Klipp Humboldt University Berlin Institute for Biology Theoretical Biophysics Yeast Cell as an Osmometer Media 1 Media 2 50µm Eriksson, Lab on
More informationContents. Preface XI Symbols and Abbreviations XIII. 1 Introduction 1
V Contents Preface XI Symbols and Abbreviations XIII 1 Introduction 1 2 Van der Waals Forces 5 2.1 Van der Waals Forces Between Molecules 5 2.1.1 Coulomb Interaction 5 2.1.2 Monopole Dipole Interaction
More informationOptical Trapping. The catalyst which motivated the development of optical trapping is often
DeSantis 1 Optical Trapping The catalyst which motivated the development of optical trapping is often attributed to James Clark Maxwell when he unveiled the concept of radiation pressure. Apart from the
More informationSTM: Scanning Tunneling Microscope
STM: Scanning Tunneling Microscope Basic idea STM working principle Schematic representation of the sample-tip tunnel barrier Assume tip and sample described by two infinite plate electrodes Φ t +Φ s =
More informationProtein Folding & Stability. Lecture 11: Margaret A. Daugherty. Fall How do we go from an unfolded polypeptide chain to a
Lecture 11: Protein Folding & Stability Margaret A. Daugherty Fall 2004 How do we go from an unfolded polypeptide chain to a compact folded protein? (Folding of thioredoxin, F. Richards) Structure - Function
More informationAFM: Atomic Force Microscopy II
AM: Atomic orce Microscopy II Jan Knudsen The MAX IV laboratory & Division of synchrotron radiation research K522-523 (Sljus) 4 th of May, 2018 http://www.sljus.lu.se/staff/rainer/spm.htm Last time: The
More informationAnalyzing Ion channel Simulations
Analyzing Ion channel Simulations (Neher and Sakmann, Scientific American 1992) Single channel current (Heurteaux et al, EMBO 2004) Computational Patch Clamp (Molecular Dynamics) Atoms move according to
More informationProteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability
Proteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability Dr. Andrew Lee UNC School of Pharmacy (Div. Chemical Biology and Medicinal Chemistry) UNC Med
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature09450 Supplementary Table 1 Summary of kinetic parameters. Kinetic parameters were V = V / 1 K / ATP and obtained using the relationships max ( + m [ ]) V d s /( 1/ k [ ATP] + 1 k ) =,
More informationSimple Harmonic Motion and Damping
Simple Harmonic Motion and Damping Marie Johnson Cabrices Chamblee Charter High School Background: Atomic Force Microscopy, or AFM, is used to characterize materials. It is used to measure local properties,
More informationEquivalent Circuit Model of the Neuron
Generator Potentials, Synaptic Potentials and Action Potentials All Can Be Described by the Equivalent Circuit Model of the Membrane Equivalent Circuit Model of the Neuron PNS, Fig 211 The Nerve (or Muscle)
More informationSOLID STATE PHYSICS PHY F341. Dr. Manjuladevi.V Associate Professor Department of Physics BITS Pilani
SOLID STATE PHYSICS PHY F341 Dr. Manjuladevi.V Associate Professor Department of Physics BITS Pilani 333031 manjula@bits-pilani.ac.in Characterization techniques SEM AFM STM BAM Outline What can we use
More informationFigure 1.1: Flaccid (a) and swollen (b) red blood cells being drawn into a micropipette. The scale bars represent 5 µm. Figure adapted from [2].
1 Biomembranes 1.1 Micropipette aspiration 1.1.1 Experimental setup Figure 1.1: Flaccid (a) and swollen (b) red blood cells being drawn into a micropipette. The scale bars represent 5 µm. Figure adapted
More informationAFM Imaging In Liquids. W. Travis Johnson PhD Agilent Technologies Nanomeasurements Division
AFM Imaging In Liquids W. Travis Johnson PhD Agilent Technologies Nanomeasurements Division Imaging Techniques: Scales Proteins 10 nm Bacteria 1μm Red Blood Cell 5μm Human Hair 75μm Si Atom Spacing 0.4nm
More informationNanobiotechnology. Place: IOP 1 st Meeting Room Time: 9:30-12:00. Reference: Review Papers. Grade: 40% midterm, 60% final report (oral + written)
Nanobiotechnology Place: IOP 1 st Meeting Room Time: 9:30-12:00 Reference: Review Papers Grade: 40% midterm, 60% final report (oral + written) Midterm: 5/18 Oral Presentation 1. 20 minutes each person
More informationContents. xiii. Preface v
Contents Preface Chapter 1 Biological Macromolecules 1.1 General PrincipIes 1.1.1 Macrornolecules 1.2 1.1.2 Configuration and Conformation Molecular lnteractions in Macromolecular Structures 1.2.1 Weak
More informationInstitute for Electron Microscopy and Nanoanalysis Graz Centre for Electron Microscopy
Institute for Electron Microscopy and Nanoanalysis Graz Centre for Electron Microscopy Micromechanics Ass.Prof. Priv.-Doz. DI Dr. Harald Plank a,b a Institute of Electron Microscopy and Nanoanalysis, Graz
More informationBiochemistry in Singulo:
Biochemistry in Singulo: When Less Means More Carlos Bustamante University of California, Berkeley The Ensemble Approach The study of chemical transforma9ons has been dominated by the ensemble method:
More informationMagnetic Force Microscopy practical
European School on Magnetism 2015 From basic magnetic concepts to spin currents Magnetic Force Microscopy practical Organized by: Yann Perrin, Michal Staňo and Olivier Fruchart Institut NEEL (CNRS & Univ.
More informationAFM for Measuring Surface Topography and Forces
ENB 2007 07.03.2007 AFM for Measuring Surface Topography and Forces Andreas Fery Scanning Probe : What is it and why do we need it? AFM as a versatile tool for local analysis and manipulation Dates Course
More informationLecture 10 : Neuronal Dynamics. Eileen Nugent
Lecture 10 : Neuronal Dynamics Eileen Nugent Origin of the Cells Resting Membrane Potential: Nernst Equation, Donnan Equilbrium Action Potentials in the Nervous System Equivalent Electrical Circuits and
More informationMechanical Proteins. Stretching imunoglobulin and fibronectin. domains of the muscle protein titin. Adhesion Proteins of the Immune System
Mechanical Proteins F C D B A domains of the muscle protein titin E Stretching imunoglobulin and fibronectin G NIH Resource for Macromolecular Modeling and Bioinformatics Theoretical Biophysics Group,
More informationMolecular Dynamics Simulation of HIV-1 Reverse. Transcriptase
Molecular Dynamics Simulation of HIV-1 Reverse Transcriptase Abderrahmane Benghanem 1 Maria Kurnikova 2 1 Rensselaer Polytechnic Institute, Troy, NY 2 Carnegie Mellon University, Pittsburgh, PA June 16,
More informationMagnetic Force Microscopy (MFM) F = µ o (m )H
Magnetic Force Microscopy (MFM) F = µ o (m )H 1. MFM is based on the use of a ferromagnetic tip as a local field sensor. Magnetic interaction between the tip and the surface results in a force acting on
More informationPhysical aspects in the self-assembly of biological complexes
Physical aspects in the self-assembly of biological complexes Bogdan Dragnea Chemistry Department Indiana University Bloomington IN 47405 dragnea@indiana.edu Self-assembling supra-molecular systems Example
More informationMS482 Materials Characterization ( 재료분석 ) Lecture Note 11: Scanning Probe Microscopy. Byungha Shin Dept. of MSE, KAIST
2015 Fall Semester MS482 Materials Characterization ( 재료분석 ) Lecture Note 11: Scanning Probe Microscopy Byungha Shin Dept. of MSE, KAIST 1 Course Information Syllabus 1. Overview of various characterization
More informationNanopores: Solid-state nanopores for these experiments were produced by using the
Materials and Methods Nanopores: Solid-state nanopores for these experiments were produced by using the highly focused electron beam of a transmission electron microscope (TEM) to drill a single pore in
More informationSolution set for EXAM IN TFY4265/FY8906 Biophysical microtechniques
ENGLISH NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY DEPARTMENT OF PHYSICS Contact during exam: Magnus Borstad Lilledahl Telefon: 73591873 (office) 92851014 (mobile) Solution set for EXAM IN TFY4265/FY8906
More informationBringing optics into the nanoscale a double-scanner AFM brings advanced optical experiments within reach
Bringing optics into the nanoscale a double-scanner AFM brings advanced optical experiments within reach Beyond the diffraction limit The resolution of optical microscopy is generally limited by the diffraction
More informationEcole Franco-Roumaine : Magnétisme des systèmes nanoscopiques et structures hybrides - Brasov, Modern Analytical Microscopic Tools
1. Introduction Solid Surfaces Analysis Group, Institute of Physics, Chemnitz University of Technology, Germany 2. Limitations of Conventional Optical Microscopy 3. Electron Microscopies Transmission Electron
More informationThe Riboswitch is functionally separated into the ligand binding APTAMER and the decision-making EXPRESSION PLATFORM
The Riboswitch is functionally separated into the ligand binding APTAMER and the decision-making EXPRESSION PLATFORM Purine riboswitch TPP riboswitch SAM riboswitch glms ribozyme In-line probing is used
More informationScanning Force Microscopy II
Scanning Force Microscopy II Measurement modes Magnetic force microscopy Artifacts Lars Johansson 1 SFM - Forces Chemical forces (short range) Van der Waals forces Electrostatic forces (long range) Capillary
More informationGenetics 304 Lecture 6
Genetics 304 Lecture 6 00/01/27 Assigned Readings Busby, S. and R.H. Ebright (1994). Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79:743-746. Reed, W.L. and
More informationLinker Dependent Bond Rupture Force Measurements in Single-Molecule Junctions
Supplemental Information Linker Dependent Bond Rupture Force Measurements in Single-Molecule Junctions M. Frei 1, S Aradhya 1, M. S. Hybertsen 2, L. Venkataraman 1 1 Department of Applied Physics and Applied
More informationThe Powerful Diversity of the AFM Probe
The Powerful Diversity of the AFM Probe Stefan B. Kaemmer, Bruker Nano Surfaces Division, Santa Barbara, CA 93117 stefan.kaemmer@bruker-nano.com March 21, 2011 Introduction The tip allows us to measure
More informationSingle-Molecule Micromanipulation Techniques
Annu. Rev. Mater. Res. 2007. 37:33 67 First published online as a Review in Advance on January 11, 2007 The Annual Review of Materials Research is online at http://matsci.annualreviews.org This article
More informationNanoscale confinement of photon and electron
Nanoscale confinement of photon and electron Photons can be confined via: Planar waveguides or microcavities (2 d) Optical fibers (1 d) Micro/nano spheres (0 d) Electrons can be confined via: Quantum well
More informationScanning Tunneling Microscopy
Scanning Tunneling Microscopy Scanning Direction References: Classical Tunneling Quantum Mechanics Tunneling current Tunneling current I t I t (V/d)exp(-Aφ 1/2 d) A = 1.025 (ev) -1/2 Å -1 I t = 10 pa~10na
More information20.GEM GEM4 Summer School: Cell and Molecular Biomechanics in Medicine: Cancer Summer 2007
MIT OpenCourseWare http://ocw.mit.edu 20.GEM GEM4 Summer School: Cell and Molecular Biomechanics in Medicine: Cancer Summer 2007 For information about citing these materials or our Terms of Use, visit:
More informationOptical Trapping Experiment - Optical Tweezers. PHY 431 Optics, Fall 2011
Optical Trapping Experiment - Optical Tweezers PHY 431 Optics, Fall 2011 Sources: Advanced Physics Laboratory, J. Shen et al., University of Toronto Phys 2010, Optical Tweezers, Brown Universiyt Optical
More informationIntermittent-Contact Mode Force Microscopy & Electrostatic Force Microscopy (EFM)
WORKSHOP Nanoscience on the Tip Intermittent-Contact Mode Force Microscopy & Electrostatic Force Microscopy (EFM) Table of Contents: 1. Motivation... 1. Simple Harmonic Motion... 1 3. AC-Mode Imaging...
More informationQuiz 2 Morphology of Complex Materials
071003 Quiz 2 Morphology of Complex Materials 1) Explain the following terms: (for states comment on biological activity and relative size of the structure) a) Native State b) Unfolded State c) Denatured
More informationCOMPLEX EFFECTS OF MOLECULAR TOPOLOGY, LENGTH AND CONCENTRATION ON MOLECULAR DYNAMICS IN ENTANGLED DNA BLENDS
COMPLEX EFFECTS OF MOLECULAR TOPOLOGY, LENGTH AND CONCENTRATION ON MOLECULAR DYNAMICS IN ENTANGLED DNA BLENDS Students Cole E. Chapman Kent Lee Dean Henze Collaborators Doug Smith (UCSD) Sachin Shanbhag
More informationSUPPLEMENTARY INFORMATION. microscopy of membrane proteins
SUPPLEMENTARY INFORMATION Glass is a viable substrate for precision force microscopy of membrane proteins Nagaraju Chada 1, Krishna P. Sigdel 1, Raghavendar Reddy Sanganna Gari 1, Tina Rezaie Matin 1,
More informationChapter 1. Topic: Overview of basic principles
Chapter 1 Topic: Overview of basic principles Four major themes of biochemistry I. What are living organism made from? II. How do organism acquire and use energy? III. How does an organism maintain its
More information(a) (b) Supplementary Figure 1. (a) (b) (a) Supplementary Figure 2. (a) (b) (c) (d) (e)
(a) (b) Supplementary Figure 1. (a) An AFM image of the device after the formation of the contact electrodes and the top gate dielectric Al 2 O 3. (b) A line scan performed along the white dashed line
More informationOutline Scanning Probe Microscope (SPM)
AFM Outline Scanning Probe Microscope (SPM) A family of microscopy forms where a sharp probe is scanned across a surface and some tip/sample interactions are monitored Scanning Tunneling Microscopy (STM)
More informationVacuum Kelvin Force Probe Research Richard Williams August 1st 2008
Vacuum Kelvin Force Probe Research Richard Williams August 1st 2008 Introduction Kelvin Force Probe Microscopy is an analytical method to measure the contact potential difference between a reference material
More informationOptical Trapping Force on a Plasmonic Substrate
Yu Pan Master of Science Thesis Supervisor: Prof. Min Yan(KTH) Examiner: Prof. Min Qiu(KTH) TRITA-ICT-EX-2012: 107 Abstract Optical trapping is currently widely applied in the field of biotechnology, in
More informationIrradiation of Living Cells with Single Ions at the Ion Microprobe SNAKE
Vol. 109 (2006) ACTA PHYSICA POLONICA A No. 3 Proceedings of the XL Zakopane School of Physics, Zakopane 2005 Irradiation of Living Cells with Single Ions at the Ion Microprobe SNAKE A. Hauptner a, T.
More information