Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

EMC > Molecular Motors Mark Szczelkun > Flashcards

Molecular Motors Mark Szczelkun Flashcards

1
Q

What is the largest and most populated family for protein folds of motors? most common and widely-distributed

A

mononucleotide-binding fold
(P-loop NTPases)
At least 7 major lineages within the P loop NTPase fold can be defined on the basis of sequence and structural feature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the P-loop NTPase fold characterised by?

A

WALKER A motif (N terminal)
consists of a flexible loop b/w a beta strand and alpha helix
positions the triphosphate of a bound NT
GxxxxGK[T/S]

WALKER B motif
contains a conserved aspartate/glutamate residue which is situated at the end of a strand
binds water-bridges Mg2+ ion
(R/K)xxxGxxL/vhhD

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Structurally P loop NTPases can be decided into 2 groups - what are these?

A

NT KINASES and the GTPases (inc. kinesin + myosin)
the strand leading to the P loop and the Walker B strand are direct neighbours

AAA+ (inc. dynein) ABC TRANSPORTER, HELICASES, RecA/F1 ATPases
additional strand inserted between P-loop strand and the Walker B strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the extra protein domain specific to AAA+ proteins?

A

Extra secondary structure SENSOR 2

Important for how AAA+ enzymes make their ATP binding pocket

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Core fold common to lots of diff p-loop family enzymes

A

repeated alpha and beta sheets
arginine finger
sensor 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Binding and hydrolysing ATP

A

Mg/Mn dependent hydrolytic cleavage of gamma phosphate
In line nuc attack of gamma phosphate by hydroxyl ion (activated H2O)
Pentaphosphate transition state intermediate stabilised by metal ions (Mg2+ is coordinated by the O’s from the phosphate groups by the WalkerA&B motives)
WALKERA
amino group of lysine interacts with phosphates of MgATP/MgADP
Hydroxyl serine/threonine coordinates Mg2+ position
WALKERB
Asp acid in position 1 coordinates Mg2+ ion
Glutamic acid in position 2 is putative catalytic residue-helps to polarise the water molecules

Arginine finger helps put gamma phosphate in place

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Domain structure of AAA+

A

Need 2 subunits to form an ATP binding pocket. Often form cyclic structures such as hexamers or heptameters etc since as they form a ring they form an ATP binding pocket at the interface of each of these structures

Sensor II (R residue inserted into active site)
R finger
WalkerB (D/E acidic residues)
Metal ion
Sensor I
P-loop/WalkerA (conserved lysine residue-holds whole NT in place)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the coupling efficiency?

A

Number of ATPs used to make one step

tightly coupled = 1, loosely coupled > 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the duty ratio?

A

How often a motor complex remains bound to the track during its catalytic cycle (from 1-100%)

motors that act in an array e.g. muscle have a low duty ratio - do not need to maintain contact to the track

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What polymer tracks do each motor take?

A

Kinesin/Dynein MTs

Myosins Actin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What family of proteins is each motor?

A 
Kinesin/Myosin = G-protein superfamily
Dynein = AAA+ super family
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the distance b/w every alpha and beta tubulin in MTs? How many protein tracks does it have?

A

8nm
13 protofilament tracks
Equivalent motor binding sites occur every 8nm along the protofilament

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

In actin what is the distance for motor binding sites?

A

36nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What type of profile is characteristic of a protective stepping motor?

A

Staircase profile

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the differences b/w polymer binding elements in kinesin and myosin?

A

kinesin - 12 aa loop binds tubulin

myosin - 140 aa domain binds actin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are the differences b/w mechanical elements in kinesin and myosin for providing the power stroke?

A

kinesin - short neck linker

myosin - converter domain and lever arm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Kinesin ATP binding hydrolysis to drive conf. change mechanism

A

Sensors I and II recognise the gamma p of the triphosphate
If ATP is present Sensor II engages the switch and the small movements of the sensor are trasmitted to other parts of the protein via a relay helix. This changes the conf of the neck linker and the MT binding domain.

18
Q

What orientation is the docked and undocked position of the kinesin and myosin neck linker/motor…or…lever arm on tubulin / actin?

Myosins and Kinesins have the same core motor yet they are coupled to conf changes different

A

KINESIN Powerstroke to + end
ATP/ADP.Pi bound = + docked
ADP/NT free = - undocked

MYOSIN Powerstoke to + end
ADP.Pi = - end
ADP/NT free = + end

19
Q

Directionality of kinesin motor depends on…?

A

1) directionality of binding to the protofilament
2) directionality of the neck linker powerstroke
Each time ATP binds the neck linker is going in the direction you want to travel (+ for kinesin)

20
Q

Myosin V (converter domain and lever arm) what angle does the lever arm move during the powerstroke?

A

70 degrees
myosin V long lever arms results in about 37nm displacement of lever arm
Movement occurs in a similar scale to the position of binding sites along one face of actin (36nm)

21
Q

Myosin VI

A

Moves to minus end
Has additional insert domain
Has proximal tail (lever arm extension)
Had medial tail

22
Q

Myosin VI has a medial tail. What keeps this structure rigid?

A

The medial tail has an unusual stable and relatively rigid single ER/K motif-containing an alpha helix

23
Q

Myosin VI has unusual step size….why?

A

Due to lever arm extension (proximal domain 3 helical bundles unfold) plus 180degrees lever arm motion allows for large step sizes despite only 2 motifs

24
Q

How Myosin II forma filaments?

A

Coils of Myosin II filaments, helical array of myosin heads pointing outwards and exist around the whole surface of the filament (360degrees)
Can have 3-400 copies of dimeric myosins

25
Q

Muscle structure

A

Epimysium-connective tissue that holds together large muscle cells called fascicles
Fascicles- a portion of muscle, bundles of individual cells surrounded by perimysium connective tissue
Muscle fiber (cell) -sarcolemma/p.memb surrounded by endomysium.
Muscle fibers made of myofibrils

26
Q

Features of skeletal muscle cells

A

large and multinucleate
muscle forms by fusion of individual cells
cells also filled with mitochondria (need lots of ATP to drive muscle contraction)-packed in-between myofibrils

27
Q

What is one sarcomere?

A

Between z discs

series of sarcomeres repeat down each myofibril

28
Q

Z discs

A

holds the ends of actin in place and stops the ends from fraying

29
Q

What are a series of actin filaments of the same length capped by in skeletal muscle?

A 
Z discs (plus end) and tropomodulin (minus end)
Cap Z-caps end of actin
30
Q

What is the dark and light banding pattern in a skeletal muscle

A

dark-myosin (thick filaments)
light-actin (thin filaments)
very dark band where there is overlap

31
Q

What is titin in skeletal muscle?

A

series of protein folds at ends of myosin
large single protein made up from a series of folds
molecular spring which is responsible for the passive elasticity of muscle
attaches to to myosin and z disc
holds whole thing together
series of repeating immunoglobulin like folds
compresses and stretches easily
LARGEST known protein made up of repeating units

32
Q

What is nebulin?

A 
wrapped around actin
long single protein 
acts as molecular ruler
fix length of actin via the length of the nebulin monomer
regular structures of the same length.
33
Q

How far is the lever arm and converter domain stroke?

A

10nm/ actin filament is moved 100Å

34
Q

What is the troponin complex?

Actin

A

Made up of 3 subunits
I-inhibitory
C-calmodulin
T-binds to tropomyosin

Tropomyosin-Wraps around the actin filament
Controls the inhibition of binding of myosin to the actin
LOW Ca2+=inhibition/RELAXATION
HIGH Ca2+=CONTRACTION troponin releases the inhibition so that actin is now available to bind to the myosin

35
Q

Transverse (T) tubules

A

Formed from invaginations of p.memb
polarisation of the T tubules due to action potential.
Invaginations carry external signals into all parts of the cell inside for coordinated contraction
Permeates into the cell

36
Q

Dynein

A

In many Euk cells there are b/w 10-15 diff dynein genes
only 1 is involved in cytoplasmic transport

Viruses are too large when they enter a Elk cell to transport to the nucleus by simple diffusion so they hijack the transport machinery to go to the nucleus

37
Q

What domain of the motor in Dynein does the strut/butress stick out of?

A 
strut/butress from AAA+ domain 5 links to stalk with MTBD
linker domain (lever arm equivalent) runs across face of AAA+ hexamer and carries out the conf change that produces mechanical motion
38
Q

What is the principle ATPase site in the dynein motor?

A 
AAA1 - ATP binds and only hydrolyses here
Each AAA+ module contains a large and small subdomain
Important residues in the large and small subdomains and the arginine finger from AAA2L
Whole system is coupled. ATP binds to only 1 domain, conf change is coupled to the other domains next to it
ATP binding sites are b/w domains and are equivalent to separate subunits in a separated AAA+
39
Q

Motor domain AAA+ dynein and coil coil domains

A

Arg finger senses terminal phosphate in ATP
Needed for catalysis and supplied by adjacent large domain from next subunit in the hexameric motor
Binding of ATP WEAKENS binding to MT
conf changes occur in butress domain and pushes against the coil coil

2 alpha helices = coil coils are generally very stable, inner face of helix has hydrophobic residues that pack against one another and stabilise it. HOWEVER in these coil coils there are a few hydrophilic amino acids that exist which allow the structure to SLIDE

40
Q

What is step size of dynein

A

16nm hand over hand
however step size is more variable and back steps are frequent
2 heads don’t seem to be coordinated
Note a significant number of steps ate >30nm
AXIAL path for dyenien is more variable (looks drunk)-can step between protofilaments
Could be important to allow dyne to by pass on coming kinesin motors

41
Q

Coupling dynein motions to motion along Mts-Additional proteins

A

DYNACTIN multi subunit complex required for vast majority of dynein functions in cells. Also binds kinesin-2
BICAUDAL-D2 (BICD2) Acts as an adaptor b/w dynein and a wide range of cargos, forms coil coiled homodimer

These two proteins convert dynein into a highly processive motor.

EMC (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions