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Crystallization Laboratory. The agony and the ecstasy of protein crystallization M230D,Jan 2008. Goal: crystallize Proteinase K and its complex with PMSF. Non-specific serine protease frequently used as a tool in molecular biology. PMSF is a suicide inhibitor. Toxic!

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crystallization laboratory

Crystallization Laboratory

The agony and the ecstasy of protein crystallization

M230D,Jan 2008

goal crystallize proteinase k and its complex with pmsf
Goal: crystallize Proteinase K and its complex with PMSF
  • Non-specific serine protease frequently used as a tool in molecular biology.
  • PMSF is a suicide inhibitor. Toxic!
  • Number of amino acids: 280
  • Molecular weight: 29038.0
  • Theoretical pI: 8.20

MAAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASH

PEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNGS

GQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVA

VAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTSILST

WIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACRYIADTANKGDLSNIPF

GTVNLLAYNNYQA

Ala (A) 33 11.8%

Arg (R) 12 4.3%

Asn (N) 17 6.1%

Asp (D) 13 4.6%

Cys (C) 5 1.8%

Gln (Q) 7 2.5%

Glu (E) 5 1.8%

Gly (G) 33 11.8%

His (H) 4 1.4%

Ile (I) 11 3.9%

Leu (L) 14 5.0%

Lys (K) 8 2.9%

Met (M) 6 2.1%

Phe (F) 6 2.1%

Pro (P) 9 3.2%

Ser (S) 37 13.2%

Thr (T) 22 7.9%

Trp (W) 2 0.7%

Tyr (Y) 17 6.1%

Val (V) 19 6.8%

it is the order of a crystal that ultimately determines the quality of the structure
It is the “order” of a crystal that ultimately determines the quality of the structure.

Order- describes the degree of regularity (or periodicity) in the arrangement of identical objects.

One dimensional order

Two dimensional order

supersaturated

protein solution.

Three dimensional order

DISORDERED

ORDERED

protein crystals are ordered periodic arrays of protein molecules
Protein crystals are ordered (periodic) arrays of protein molecules.

Order- describes the degree of regularity (or periodicity) in the arrangement of identical objects.

One dimensional order

Two dimensional order

supersaturated

protein solution.

Three dimensional order

DISORDERED

ORDERED

order is perfect when the crystallized object is regularly positioned and oriented in a lattice

c

a

b

“Order” is perfect when the crystallized object is regularly positioned and oriented in a lattice.
when a crystal is ordered strong diffraction results from constructive interference of photons

7

6

5

4

3

2

1

When a crystal is ordered, strong diffraction results from constructive interference of photons.

Interference is constructive because path lengths differ by some integral multiple of the wavelength (nl).

detector

5

crystal

4

3

2

6

1

5

4

3

Incident X-ray

2

1

In phase

This situation is possible only because the diffracting objects are periodic.

nonregularity in orientation or position limits the order and usefulness of a crystal
Nonregularity in orientation or position limits theorderand usefulness of a crystal.

Translational disorder

Rotational disorder

Perfect order

Disorder destroys the periodicity leading to

Streaky, weak, fuzzy, diffraction.

when a crystal is disordered poor diffraction results from destructive interference of photons
When a crystal is disordered, poor diffraction results from destructive interference of photons.

Interference is destructive because path lengths differ by non integral multiple of the wavelength (nl).

detector

7

6

crystal

2

9

Incident X-rays

.

Out of phase

.

Path lengths differences are not nl because of disorder.

crystal order and resolution improves with increasing number of lattice contacts
Crystal order (and resolution) improves with increasing number of lattice contacts
  • Trypsin (1gdn)
  • 0.8 Å resolution
  • Solvent content=36.6%
  • Potassium channel (1p7b)
  • 3.7 Å resolution
  • Solvent content=77.7%
lattice contacts can form only where the protein surface is rigid
Lattice contacts can form only where the protein surface is rigid.

By exposing rigid surface area, you enable new crystal forms previously unachievable.

  • Eliminate floppy, mobile termini (cleave His tags)
  • Express individual domains separately and crystallize separately, or…
  • Add a ligand that bridges the domains and locks them together.
  • Mutate high entropy residues (Glu, Lys) to Ala.

Illustrate this.

is crystallization spontaneous under biological conditions

Crystallization

Solubilization

Is crystallization spontaneous under biological conditions?

A lysozyme crystal

Orientation and position of

molecules are locked in a 3D array

High “order”

Solvated lysozyme

monomers

Random orientation and position

the barriers to crystallization
The barriers to crystallization

Unstable

nucleus

  • Energy penalty
    • Lose 3 degrees of freedom in orientation of protein molecules
    • Lose 3 degrees of freedom in translation of protein molecules

1 crystal

(lysozyme)N

  • Energy gained
    • Some entropy gained by freeing some surface bound water molecules.
    • Small enthalpic gain from crystal packing interactions.

N soluble

lysozyme

molecules

DG

  • Also, nucleation imposes a kinetic barrier.
    • Unstable because too few molecules are assembled to form all lattice contacts.

nM→Mn

the barriers to crystallization15
The barriers to crystallization

Unstable

nucleus

DG is decreased and the nucleation barrier lowered by increasing the monomer concentration [M].

nM→Mn

DG=DGo+RTln( [Mn]/[M]n )

Lesson:To crystallize a protein, you need to increase its concentration to exceed its solubility (by 3x). Force the monomer out of solution and into the crystal. Supersaturate!

N soluble

lysozyme

molecules

1 crystal

(lysozyme)N

DG

nM→Mn

methods for achieving supersaturation
Methods for achieving supersaturation.

1) Maximize concentration of purified protein

  • Centricon-centrifugal force
  • Amicon-pressure
  • Vacuum dialysis
  • Dialysis against high molecular weight PEG
  • Ion exchange.
  • Slow! Avoid precipitation. Co-solvent or low salt to maintain native state.
  • We are going to dissolve lyophilized protein in a small volume of water.

Concentrate

protein

methods for achieving supersaturation17
Methods for achieving supersaturation.

2) Add a precipitating agent

  • Polyethylene glycol
    • PEG 8000
    • PEG 4000
  • High salt concentration
    • (NH4)2SO4
    • NaH2PO4/Na2HPO4Polyethylene glycol
  • Small organics
    • ethanol
    • Methylpentanediol (MPD)

PEG

Polymer of ethylene glycol

Precipitating agents monopolize water molecules, driving proteins to neutralize their surface charges by interacting with one another.

systematic vs shotgun screening
Systematic vs. Shotgun Screening
  • Shotgun- for finding initial conditions, samples different preciptating agents, pHs, salts.
  • Systematic-for optimizing crystallization condtions.

First commercially

Available crystallization

Screening kit.

Hampton Crystal Screen 1

methods for achieving supersaturation19
Methods for achieving supersaturation.

Drop =½ protein + ½ reservoir

3) Further dehydrate the protein solution

  • Hanging drop vapor diffusion
  • Sitting drop vapor diffusion
  • Dialysis
  • Liquid-liquid interface diffusion

2M ammonium sulfate

Note: Ammonium sulfate concentration is 2M in reservoir and only 1M in the drop.

With time, water will vaporize from the drop and condense in the reservoir in order to balance the salt concentration.—SUPERSATURATION is achieved!

practical considerations
Practical Considerations
  • Begin with reservoirs:
  • pipet req’d amount of ammonium sulfate to each well.
  • Pipet req’d Tris buffers, to each well
  • Same with water.
  • Then swirl tray gently to mix.
  • When reservoirs are ready, lay 6 coverslips on the tray lid,
  • then pipet protein drops on slips and invert over reservoir.
  • Only 6 at a time, or else dry out.

Linbro or VDX plate

each pipetor has a different range of accuracy
Each pipetor has a different range of accuracy

P20

P200

P1000

200-1000uL

20-200uL

1-20uL

withdrawing and dispensing liquid 3 different positions

P1000

P1000

P1000

Withdrawing and Dispensing Liquid.3 different positions

Start position

First stop

Second stop

0

2

7

0

2

7

0

2

7

|||||

|||||

|||||

withdrawing solution set volume then push plunger to first stop to push air out of the tip

P1000

Withdrawing solution: set volume, then push plunger to first stop to push air out of the tip.

Start position

First stop

Second stop

0

2

7

|||||

-

-

-

-

50 mL

dip tip below surface of solution then release plunger gently to withdraw solution

P1000

Dip tip below surface of solution. Then release plunger gently to withdraw solution

Start position

First stop

Second stop

0

2

7

|||||

to expel solution push to second stop

P1000

To expel solution, push to second stop.

Start position

First stop

Second stop

0

2

7

|||||

when dispensing protein just push to first stop bubbles mean troubles

P1000

When dispensing protein, just push to first stop.Bubbles mean troubles.

Start position

First stop

Second stop

0

2

7

|||||

hanging drop vapor diffusion step two
Hanging drop vapor diffusionstep two

Pipet 2.5 uL of concentrated protein (50 mg/mL) onto a siliconized glass coverslip.

Pipet 2.5 uL of the reservoir solution onto the protein drop

2M ammonium sulfate

0.1M buffer

BUBBLES MEAN TROUBLES

Expel to 1st stop, not 2nd stop!

hanging drop vapor diffusion step three
Hanging drop vapor diffusionstep three
  • Invert cover slip over reservoir quickly & deliberately.
    • Don’t hesitate when coverslip on its side or else drop will roll off cover slip.
    • Don’t get fingerprints on coverslip –they obscure your view of the crystal under the microscope.
dissolving proteinase k powder
Dissolving Proteinase K powder
  • Mix gently
    • Pipet up and down 5 times
    • Stir with pipet tip gently
    • Excessive mixing leads to xtal showers
  • No bubbles

5.25 mg ProK powder

100 uL water

4 uL of 0.1M PMSF

50 mg/mL ProK

dissolving proteinase k powder40
Dissolving Proteinase K powder
  • Mix gently
    • Pipet up and down 5 times
    • Stir with pipet tip gently
    • Excessive mixing leads to xtal showers
  • No bubbles

Remove

50 uL

Add to 5 uL

of 100 mM PMSF

50 mg/mL ProK

55 uL of

50 mg/mL ProK+PMSF complex

proteinase k time lapse photography
Proteinase K time lapse photography
  • Covers first 5 hours of crystal growth in 20 minute increments

500 mm

why are heavy atoms used to solve the phase problem
Why are heavy atoms used to solve the phase problem?
  • Phase problem was first solved in 1960. Kendrew & Perutz soaked heavy atoms into a hemoglobin crystal, just as we are doing today. (isomorphous replacement).
  • Heavy atoms are useful because they are electron dense. Bottom of periodic table.
  • High electron density is useful because X-rays are diffracted from electrons.
  • When the heavy atom is bound to discrete sites in a protein crystal (a derivative), it alters the X-ray diffraction pattern slightly.
  • Comparing diffraction patterns from native and derivative data sets gives phase information.
why do heavy atoms have to be screened
Why do heavy atoms have to be screened?
  • To affect the diffraction pattern, heavy atom binding must be specific
    • Must bind the same site (e.g. Cys 134) on every protein molecule throughout the crystal.
    • Non specific binding does not help.
  • Specific binding often requires specific side chains (e.g. Cys, His, Asp, Glu) and geometry.
    • It is not possible to determine whether a heavy atom will bind to a protein given only its amino acid composition.
before 2000 trial error was the primary method of heavy atom screening
Before 2000, trial & error was the primary method of heavy atom screening
  • Pick a heavy atom compound
    • hundreds to chose from
  • Soak a crystal
    • Most of the time the heavy atom will crack the crystal.
    • If crystal cracks, try lower concentration or soak for less time.
    • Surviving crystal are sent for data collection.
  • Collect a data set
  • Compare diffraction intensities between native and potential derivative.
  • Enormously wasteful of time and resources. Crystals are expensive to make.

How many crystallization plates does it take to find a decent heavy atom derivative?

heavy atom gel shift assay
Heavy Atom Gel Shift Assay
  • Specific binding affects mobility in native gel.
  • Compare mobility of protein in presence and absence of heavy atom.
  • Heavy atoms which produce a gel shift are good candidates for crystal soaking
  • Collect data on soaked crystals and compare with native.
  • Assay performed on soluble protein, not crystal.

None Hg Au Pt Pb Sm

procedures
Procedures
  • Just incubate protein with heavy atom for a minute.
    • Pipet 3 uL of protein on parafilm covered plate.
    • Pipet 1 uL of heavy atom as specified.
    • Give plate to me to load on gel.
  • Run on a native gel
  • We use PhastSystem
  • Reverse Polarity electrode
  • Room BH269 (Yeates Lab)