Lect 21-22 Molecular Machines_print

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4/24/20

MSE 598/494 Bio-inspired Materials and Biomaterials MSE 598/494 Bio-inspired Materials and Biomaterials

Instructor: Ximin He

TA: Xiying Chen Email: [email protected]

2014-04-22

Lecture 21-22

Bioinspired Molecular Machines

What you will learn in the next 60 minutes

Molecular Machines

I. MECHANICAL EFFECTS IN BIOLOGICAL MACHINES

• Skeletal Muscle

• Kinesin

• Rotaxane

II. THEORETICAL CONSIDERATIONS

FLASHING RATCHETS

III. SLIDING MACHINES: rotaxane

– Example 1. Synthetic Molecular Muscle

– Example 2. Shuttle

– Example 3. Walking

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Motion Generation - via Mechanical Machines

Motion:Coherent change in location of one body with respect to another

3

• Macro-scale:

Generated by mechanical machines

• Micro/Nano-scale:

Molecular machines - natural & synthetic(functional subunits for action with bio-inspireddesign)

video

Realizing Controllable Movements – Mimicking & Innovation

• While lift and control are clear

emulations, airplanes do notpropel through the skies like birds.

• “Where biology shows us that

rotary motors and walkingmachines are possible, molecular

machinery access to the samefunctionality may be realized in

different forms and with differentbuilding blocks.”

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Different types of motion in biology and artificial systems

Leeuwenhoek’s “little animals”Skeletal muscle’s sarcomere kinesin

Whitesides’s

autonomous

swimmers

Mallouk’s remote-controlled

catalytic nanorods

Sauvage’s molecular muscles

Stoddart’s nanoelectrochemical system (NEMS)

Stojanovic’s

DNA robot

Leigh’s synthetic walker

I. MECHANICAL EFFECTS IN BIOLOGICAL

MACHINES

• Skeletal Muscle

• Kinesin

• Rotaxane

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1. Skeletal Muscle - Structure and Function

• The contraction and extension of a sarcomere is induced by themyosin head groups acting on actin filaments.

7

video

1. Skeletal Muscle - myosin crossbridge cycle

The movement of myosin motors along actin filaments involves a complex

cycle of :

• nucleotide-binding state, ATP hydrolysis

• changes in conformation, actin affinity • Pi and ADP disassociation

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Fast response

Highly efficient

ATP binding

‐detachment

energizing

‐attachment

power strokePi leaving

www.bms.ed.ac.uk ADP leaving



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2. Kinesin

Kinesin, a motor protein, walks by itself • utilizing ATP hydrolysis to power its movement

• walks hand-over-hand along a microtubule

• hauling vesicle cargo essential to life’s functions – uni-directionality

9

video

ATP/ADP binding and then hydrolysis in the head that is bound to the microtubule allow the unbound head bearing ADP to take a step forward. The step involves a diffusional search by the unbound head for the adjacent tubulin

unit to settle on to. The front head then releases its ADP, causing it to bind more strongly to the microtubule.The back head subsequently releases Pi, allowing it to lift off from the microtubule in a sequence that may be gated

by the preceding event. ATP can then bind to the head attached to the microtubule, bringing the motor back to its

initial state.

2. Kinesin



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3. F1-ATP Synthase

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• not coupled to any large-scale work-generating process,

• nor is its biological operation principally driven by ATP hydrolysis

• powered by harnessing a chemical potential created by a pH gradient and using it

to induce rotational motion accompanied by the synthesis of ATP

video

(a) Free ADP binds in empty α / β subunits

( α / β E ), forming a complex with them

( α / β DP ).

Rotation of the ATPase γ subunit is driven

by H+ transport across a membrane,permitting the release of synthesized ATP

from the α / β TP subunit.

(b) Surface-mounted ATPase rotates anactin filament as captured by (c)fluorescence images.

Common Features of Biological Machines (biomotors)

1. movements: There is clear movement of one component with respectto another

2. solid supports: The motors and machines are usually interfaced with alarge support material.

3. ATP hydrolyses: Fuel in the form of ATP hydrolysis powers themovements.

4. binding/debinding Events: Sequential binding and debinding eventsare also involved.

5. use of thermal energy: The machines use ambient thermal energy andBrownian motion to move.

6. chemical cycles: The biomotor performs a cycle of motion that is

intrinsically governed by chemistry.

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II. THEORETICAL CONSIDERATIONS:

FLASHING RATCHETS

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• Directional motion: against accepted law in Chemistry

• In biomotors, the state of the system is different in the forward and backward steps

Change induced in many ways:• binding,• ATP hydrolysis,• redox changes,• light absorption,• protonations

cm

Feynman’s though t experiment of a molecular-scale ratchet:

To the left, they get recaptured in the original well when the sawtooth is reinstated. But to the right, they could

progress to the adjacent location once the sawtooth is flashed on again. Thus, “flashing” the potential energy

surface “on” and “off” on appropriate time scales permits limited periods of diffusion, where probability dictates

the particle will most likely maintain its position or move unidirectionally to the right.

(a) The energy profile of movement in a

CM-scale macroscopic ratchet thatachieves directional movement. (b) a

nanoscale ratchet that does not. (c) A

flashing ratchet along with Brownian

motion circumvents the principle of

microscopic reversibility to drive

movement to the right.

• There are two double-well potentials:

• The stimulus acts on the thermodynamics of the

energy wells by turning states “off” and “on,” aproperty known as bistability.

• At the same time, different pathways are switched

“off” and “on” by making the kinetic barrierslarger and smaller, a property defined as bilability.

• Thus, unidirectional motion can be attainedfollowing (1) stimulation, (2) move right, (3)

remove stimulation, (4) move right, and continuecycling periodically.

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At the molecular level, flat potential surfaces are extremely rare, and so,

unidirectional motion can be achieved by switching between two differentdouble-well potentials.

• Biomotors operate under similar conditions but greater complexity

• Bioinspired machines – emulating motion at simpler level



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III. SLIDING MACHINES

• Linear Machines: Rotaxanes• Bistable rotaxanes are elementary machines that display linear motion.

• Composed of ring interlocked around a dumbbell with two stations

The ring’s affinity for one station is

designed to respond to stimulation

by photons, electrons, protons, or other

chemistries, in order to move the ring

controllably from one station to the

other.

When the stimulation is removed,

the ring moves back again. Essentially,

ATP has been replaced with a differentfuel source.

Linear Machines: Rotaxanes

Oxidation and reduction of copper causes the movement of the macrocycle, which is

based on the stereochemical preferences of Cu(I) and Cu(II). The larger macrocycle

translates more rapidly across the dumbbell than the smaller one.



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Example 1. Artificial Muscle

The CBPQT4+ macrocycles to move in/out-ward in this molecular muscle via oxidation/reduction of the two TTF units

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TTF oxidation-driven movements

rotaxanes are attached to a

cantilever via the disulfide

linker on the CBPQT4+





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Reading Resources

Natural:

• TEDxSydney - Drew Berry - Astonishing Molecular Machines

http://youtu.be/DfB8vQokr0Q

(Malaria, Mosquito bite, Drew Berry – a biomedical animator whose scientifically

accurate and aesthetically rich visualisations reveal the microscopic world inside our

bodies to a wide range of audiences)

Artificial:

• “Engineering Applications of Biomolecular Motors” H. Hess, Annu. Rev.

Biomed. Eng. 2011

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Summary of the Course

• What are Bioinspired Engineering and Bioinspried Materials? – Understanding natural biological systems

– Taking their strategy to create/engineer new material (systems)

– Structure – Property -- Functions

• Wide Scales:

System - organism – organ – tissue – cell – proteins - DNA - molecules

• Wide Variety…

shapes?

material/composition?

…

Biomineralization

Protein templated assembled and

crystalized CaCO3

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Why can it walk on water?

What’s the feature on the feet?…

Superhydrophobic materials

Common Basilisk

One of the few animal species that can walk on water 25

Why this shape?

For beauty?

…

or sailing.

Velella velellasea raft, by-the-wind sailor, purple sail

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Signaling?

For prey? communication?…

Bioluminescent

light emitting materials

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Iridescent color

From pigment? or structure?…

Structuring color

Bio-optics, photonics28



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Both self-cleaning surface?

…

Dynamic self-cleaningand Drag reduction

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Both Adhesive?

Dry v.s. Under water

…Structure

v.s.

Chemistry30



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Course Topics

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Topics:

* Stimuli-Responsive Hydrogels

Biomimetic Self-oscillating Polymer gels

Stimuli-Responsive Surfaces in Biomed App

Stimuli-responsive Conjugated Polymers: from electronic noses to

Artificial Muscles

* Artificial Photosynthesis

* Biological geological technic,

* Neural networks and bioinspired computers

* Biomimetic Surfaces I: Adhesion & Wetting

Color-Photonic Materials

Biomimetic Surfaces II: Biosensing

Cell-Surface Interaction

* Biomineralization I: Protein

Biomineralization II: Organism

* Tissue Engineering: OrgansCell seeding; TE scaffolds

* Self-assembly I: Self-assembled structureSelf-assembly II: Principles of cooperativity in Bioinspired Self-

assembling systems

* Bioinspired Molecular Machines

Bioinspired Materials & Biomaterials

Subject Focus:

1. developing a fundamental understanding of the synthesis, directed self-assembly and hierarchical organization of natural occurring materials,

2. using this understanding to engineer new bioinspired artificial materials for

diverse applications.

Content:

provide a broad overview of these most recent advances in bio-inspired materials,covering:

natural materials, biomimetic and bioinspired artificial materials

with an emphasis on:synthesis, processing, hierarchical design from the nano- to the macro-scale,

properties and characterizations, as well as real-life applications

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At the end of the course

• Better understanding of

– the biologically inspired materials and biomaterials, as well as hybridmaterial systems

– fundamental principle of material design

– synthesis and assembly

– characterization of structure, properties and behaviors

• Be inspired to innovate your own new materials

– propose original research topics

– study natural biological systems and select and design materials forspecific applications

– determine processing conditions that leads to materials for specific

applications

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Structure of the Course

Lecture

Homework

Lit RevOriginalresearch

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Basic Concepts & knowledge

Broadening up-to-date research

Try your bioinspired idea

Review & deeper understand



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Proposal

Template:1. Abstract (1 page)

2. Project Description ( 8-11 for grads, 6-9 for undergrads)

– clearly state your Novelty and Research Plan

3. Summary (1 page)

NEW FORMATTING!

• Font: Arial 11 or Times new Roman 12

• Spacing: 1.5 line

* Changes highlighted in red

Presentations

• Best Proposal Presentation Award (x2)

– A prize for a student with the highest evaluation in each group

– Evaluation Criteria:

Significance/Impact (5)

Novelty/Originality (5)

Feasibility/Practicality (5)

Structured/Comprehensive (5) – clearly state your Novelty and Research Plan

• Time: 10-minute presentation + 3-minute questions.

• Ready for presentation:

– Please upload your presentations by 11:30 AM on the day of your presentation( Apr 19 or May 1 ) to Google Drive. I’ll copy them to the computer in classroom.

– Otherwise, bring your presentation in USB stick and copy it to the computer in

classroom by 1:20 PM on the day of your presentation.

Documents

Lect 21-22 Molecular Machines_print