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Taking Liberties with The Leaning Tower of PISA • The !-helix casts a projection onto the Plain of PISA • PISA - Polar Index Slant Angles • The helix is stabilized by hydrogen bonds between the carbonyl of residue ‘i’ and the amide nitrogen of residue ‘i+4’ Wang et al., 2000 JMR 144:162-167. Wang et al., 2000 JMR 144:162-167. Marassi Marassi & & Opella Opella, 2000 JMR 144: 150-155. , 2000 JMR 144: 150-155. From PISA Wheels to From PISA Wheels to High Resolution High Resolution Protein Structure Protein Structure

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Page 1: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Taking Liberties with

The Leaning Tower of

PISA

• The !-helix casts a

projection onto the Plain

of PISA

• PISA - Polar Index Slant Angles

• The helix is stabilized by

hydrogen bonds

between the carbonyl

of residue ‘i’ and

the amide nitrogen of

residue ‘i+4’

Wang et al., 2000 JMR 144:162-167.Wang et al., 2000 JMR 144:162-167.Marassi Marassi & & OpellaOpella, 2000 JMR 144: 150-155., 2000 JMR 144: 150-155.

From PISA Wheels toFrom PISA Wheels to

High ResolutionHigh Resolution

Protein StructureProtein Structure

Page 2: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

The Cellular Environment

Complex

Diverse

and

Heterogeneous

Rough ER

SUSUMU ITO

TINA CARVALHO

MitochondrionD.S. FRIEND

Page 3: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

The Membrane Environment

• Complex, Diverse, and Heterogeneous

• Membranes are densely packed with proteins;

membranes in eukaryotes are compartmentalized;

lipids in the leaflets are different

Engelman (2006) Nature 438:578

Page 4: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Amino Acids

-350

-300

-250

-200

-150

-100

-50

0

50

100

150

200

250

Percentage Increase

Over Water Soluble

Proteins

Percentage Increase

Over Membrane

Proteins

Amino Acid Composition Comparison of Membrane

& Water Soluble Proetins• This is the compo- sition for the TM regions

• Non polar AA is more common in MP

• Some polar AA are also more common in MP e.g. Trp, Gly

• But others are not such as Asn and Gln

• The only charged residue that is as common in MP is His

• Many of these stand-out amino acids have special functions in MP

Eilers et al., 2003

Page 5: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Membrane Protein Environment

Dielectric

Constant: 2 to 220 80

[H2O]: 10-6 to 55 M 55 M

Fluidity Scd: 0 - 0.4 0

Lateral

Pressure: 1 to 300 atm 1 atm

Membrane

Environment

Aqueous

Environment

Weiner & White (1992) Biophys J. 61:

434-447

»» very important and difficult to mimic the

membrane environment

»» necessary to characterize the structure,

dynamics and function of membrane proteins in a lipid environment - solid state NMR is

becoming the Gold Standard for Membrane Protein Structural Biology.

• Variable Lipid and Protein Composition.

• Gradients in: Dielectric constant, Water

concentration, Fluidity, and Lateral Pressure.

• Protein Structure and Function are Modulated by

the Membrane Environment

Page 6: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Protein Structural and

Functional Sensitivity

to Environment

• Gramicidin A: Changes in Lipid

Composition alters the potential energy

profile making cation entry and exit

the primary barrier instead of the

central barrier.

• Lac Permease: Changes

in Lipid Head Group

Composition alters the

transmembrane helical

topology and destroys

Lactose transport

Abramson et al., (2003)

Science 301:610

Page 7: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

In Vitro Membrane Protein Folding - The Influence of Water

Xu & Cross, 1999 PNAS 96: 9057

Page 8: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

In Vitro Membrane Protein Folding - The Influence of Water

Xu & Cross, 1999 PNAS 96: 9057

• Dependence of structural interconversion on [H2O] in an aprotic solvent.

• Hill plot with a slope of 6.5

• Interconversion dependent of [H2O]6.5

Page 9: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Water is a Catalyst for H-bond Exchange

v ! [H2O]6.5

»» Water elevates the free

energy of the ground state

»» Water lowers the free

energy of the potential

energy barrier

»» Water is not consumed

in the process

»» Hence water is a

catalyst

»» Analogous to acid

catalyzed covalent bond

rearrangements

»» Not much water in the

membrane interstices

Page 10: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Trapped Conformation in a Lipid Bilayer

»» The antiparallel structure readily (< 10 min) rearranges to form the channel state

»» The parallel structure rearranges slowly (>5000 min) to form the channel state

Page 11: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

M2 Domain

Structures

3BKD Stouffer et al., 20082H95 Hu et al., 2007

2KAD Cady et al., 2009

2RLF Schnell & Chouet al., 2008

1NYJ Nishimura et al., 2002

AMT

AMT

AMT

Page 12: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Important Points about Membrane Proteins and

their Environment

1.1. Christian B. Christian B. Anfinsen Anfinsen and the and the ““thermodynamic hypothesisthermodynamic hypothesis””: : “…“… the the

native conformation is determined by the totality of inter-atomicnative conformation is determined by the totality of inter-atomic

interactions and hence by the amino acid sequence,interactions and hence by the amino acid sequence, in a givenin a given

environment.environment.”” Science,Science, 1973 1973. --- . --- It is essential to characterizeIt is essential to characterize

membrane protein structures in an environment that is a close to themembrane protein structures in an environment that is a close to the

nativenative environment as possible.environment as possible.

2.2. Detergents provide an inferior membrane mimetic environment.Detergents provide an inferior membrane mimetic environment.

- there- there is much is much more watermore water in a detergent micelle than in a lipid bilayer. in a detergent micelle than in a lipid bilayer.

- - the the monomeric monomeric detergent concentrationdetergent concentration far exceeds that of the lipid far exceeds that of the lipid

monomeric monomeric concentration leading to concentration leading to denaturation denaturation of water solubleof water soluble

domains or detergent penetration into the protein structure.domains or detergent penetration into the protein structure.

- - detergentsdetergents represent a monolayerrepresent a monolayer and hence and hence hydrophilic residues in ahydrophilic residues in a

transmembrane helix can be transmembrane helix can be solubilized solubilized in a in a hydrophiic hydrophiic environmentenvironment

withwith only a minimal energetic penalty.only a minimal energetic penalty.

3.3. Bilayers mayBilayers may kinetically trap non-minimum energy conformationalkinetically trap non-minimum energy conformational

states.states.

Page 13: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Aligned Sample on Glass Slides• Detergent Mediated reconstitution

• Bilayer Environment

– Native like environment

– Position and orientation within bilayer attainable

– 1H/15N-PISEMA

– Oriented Bilayer samples ~1:50 molar ratio of peptide:lipid

• Proteoliposomes deposited onto thin glass slides

• Dehydrate, stack, rehydrate (50% by wt. water in sealed tube)

• 30-40 stacked slides per sample

• !5,000 bilayers per slide

– Mosaicity

• < 0.5° mosaic spread for well prepared samples

Page 14: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

PISEMA Introduction

Page 15: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Calculation of

PISA Wheels

Wang et al., (2000)

J. Magn. Reson. 144:162

Page 16: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Structure Determination from Aligned Samples

1.1. PISA wheels provide some high resolutionPISA wheels provide some high resolution

results but they represent ONLY an initialresults but they represent ONLY an initial

structural assessment from PISEMA data.structural assessment from PISEMA data.

2.2. The PISEMA restraints provideThe PISEMA restraints provide unique peptideunique peptide

plane orientations andplane orientations and structural refinement isstructural refinement is

most efficiently achieved with Restrainedmost efficiently achieved with Restrained

Molecular DynamicsMolecular Dynamics

Page 17: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

PISA Wheels observed in

Peptides and Proteins

• CorA TM2: The second of two

transmembrane helices from the Mg2+

transporter from M. tuberculosis. The

native protein is pentameric but this peptide

is monomeric

• KdpC: An 18 kDa protein with a single

transmembrane helix that forms part of the

Kdp K+ transport system in Mtb - this is a

spectrum of the full length protein.

• KdpF: Another gene product for the Kdp

complex - this one is just 4 kDa and this is

the spectrum of the full length protein

• M2-TMD: This is a spectrum of the

transmembrane helix from M2 protein of

influenza A virus that forms a tetrameric

bundle.

CorA TM2

KdpC

KdpF

M2-TMD

Page 18: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Membrane Proteins: Solid State NMR

• Sample Preparation is everything

• Homogeneous and Uniformly

Aligned Preparation

• Spectral Resolution

• Long Term Stability

• Utilized Liquid-crystalline

Lipid Bilayers

• Requires isotopic labeling

• Can obtain structural

information from 1st spectrum

• 1st Spectrum includes Structural

Restraints, but need more

• Finally build a Structural

Model

Spectra of three full length MPs in Uniformly Aligned Liquid-Crystalline Lipid Bilayers - Li et al., JACS 2007

Page 19: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

»» " values from the variation in M2-TMD CSA values

Page 20: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

»» Typical values are 17° for most residues,except for Gly that is 21°

Page 21: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

»» Typical water soluble protein helix has a # value of 12°

Page 22: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

• Note the two planes on either

side of the !-carbon, with $ angle

between the !-carbon and the N of

one amide and the % angle

between the !-carbon and the

carbonyl C of the next amide.

• The $ angle is defined

incorrectly in 90% of all

Biochemistry texts even though

the definition was changed in

1972!!

Torsion Angles in Protein Backbone

Page 23: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Rhamachandran

Diagram

$$=180°, =180°, %%=0°=0°

Page 24: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Rhamachandran

Diagram

$$=-60°, =-60°, %%=0°=0°

»»»» A rotation of 120° in A rotation of 120° in $$ results in removing the results in removing the steric steric hindrancehindrance betweenbetweenthe carbonyl and the side-chainthe carbonyl and the side-chain

Page 25: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Rhamachandran

Diagram• Many secondary structures have

a repeating set of phi/psi torsion

angles.

• However, this does not mean

that the torsion angles are

precisely the same.

• The dark purple spots indicate a

distribution of torsion angles -

even for the helical region the

distribution is large.

• Why might they not be

precisely the same?

Page 26: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Note that:

• The helix can be viewed as a

stacked array of peptide planes

hinged at the !-carbons and

approximately, but not quite

parallel to the helix.

• To achieve this secondary

structure the approximate

torsion angles are & = -65°;

' = -40° based on thousands

of water soluble protein

structures.

!-Helix

Page 27: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Helices ! Residues & Atoms per turn:! !-Helix: 3.6 residues & 13 atoms (3.613 helix)! 310-Helix: 3.2 residues & 10 atoms (3.210 helix)! (-Helix: 4.4 residues & 16 atoms (4.416 helix)

Fig. 6-06d, p.159

Kim & Cross (2004)

J. Magn. Reson. 168:

187-193.

Page 28: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Helices

Kim & Cross (2004) J. Magn. Reson. 168:187-193.

Page 29: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

The Rhamachandran-delta diagram

•• For regular helical For regular helical

structures it is possible tostructures it is possible to

draw lines of constantdraw lines of constant

peptide plane tilt anglepeptide plane tilt angle

onto the Rhamachandranonto the Rhamachandran

diagram.diagram.

•• Very approximate Very approximate

positions of 3positions of 310, , !! and and ((

helices is displayedhelices is displayed

•• Note that the Note that the ( helix can helix can

have a negative peptidehave a negative peptide

plane tilt angleplane tilt angle

Page 30: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Helices

Kim & Cross (2004) J. Magn. Reson. 168:187-193.

PISEMA SimulationsPISEMA Simulations

Helical WheelsHelical Wheels

331010 !! ((

Page 31: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Helices

Kim & Cross (2004) J. Magn. Reson. 168:187-193.

331010 !! ((

Pisema Pisema SimulationsSimulations

Page 32: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Kim & Cross (2002) J. Magn. Reson. 168:187-193.

PISA Wheels as

a function of

delta

•• Here we Here we illus-illus-

trate trate that thethat the

rotational rotational direc-direc-

tion tion of the of the sequen-sequen-

tial tial patternpattern

reverses when thereverses when the

delta value bdelta value be-e-

comes comes negative.negative.

Page 33: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Observed PISA Wheels: # = 9±4°; $=-60°, %=-45°»» It is clear that the torsion angles are very uniform It is clear that the torsion angles are very uniform in a membranein a membrane

environment for a variety of proteins and that these helices are slightlyenvironment for a variety of proteins and that these helices are slightlydifferent from the helices of water soluble proteins.different from the helices of water soluble proteins.

Page 34: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Helical Torsion Angles

»» The difference between $,%

angles of -40°, -65° and -45°, -60°

is quite small, but the carbonyl

oxygen becomes less exposed.

»» Rhamachandran diagram

showing the # values for the tilt

of the carbonyl bond with respect

to the helix axis

Page 35: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Torsion Angle Data for Membrane Proteins from

x-ray crystallographic data

»» High resolution High resolution crystalcrystaldata supports verydata supports veryuniform torsion auniform torsion angles inngles insharp contrast with thesharp contrast with thewater soluble proteins.water soluble proteins.

•• Data for trans-membrane Data for trans-membrane!!-helices -helices as a function ofas a function ofcrystallographic resolution.crystallographic resolution.

Page et al., 2008 Structure 16:1-11

Page 36: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Dependence of PISA Wheels on Local Conformation: The Source of

Resonance Dispersion

$ = -60 ± 0°

% = -45 ± 0°

$ = -60 ± 4°

% = -45 ± 4°

$ = -60 ± 8°

% = -45 ± 8°

Page et al., 2007MRC 45:S2-S11

Page 37: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Calculation of PISA Wheels

»» Note that the dispersion scales down as the wheel scales down

Page et al., 2007 MRC 45:S2-S11

Page 38: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Why the Dramatic Reduction in

Torsion Angle Scatter?

»» Approximately a factor of four reduction Approximately a factor of four reductionin scatter forin scatter for moderate resolution structuresmoderate resolution structures

Page et al., 2008 Structure 16:1-11

»» Strengthened h-

bonds in a low

dielectric

environment

»» Lack of water and

protic sidechains to

destabilize backbone

h-bonds

Page 39: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Hydrogen Bond geometryNHNH••••••OO COCO••••••NN

AnglesAngles + H+ H••••••O dist.O dist.

•• NH NH••••••O angles areO angles aretypicallytypically !!140°140°

•• CO CO••••••N angles areN angles aretypically between 140typically between 140and 160°and 160°

•• H H••••••O distances areO distances aretypically between 2.0typically between 2.0and 2.4Åand 2.4Å

»» A preferred region of»» A preferred region of$/%$/% space is definedspace is defined

Page et al., 2008 Structure 16:1-11

Page 40: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Important Points about PISA Wheels from

Transmembrane Helices

1.1. There is considerable scatter in the observed data - such scatter can beThere is considerable scatter in the observed data - such scatter can be

completely explained by ± 4° in completely explained by ± 4° in ## equivalent to ± 5° in average torsion equivalent to ± 5° in average torsion

angles. Obviously thereangles. Obviously there are other sources for this scatter andare other sources for this scatter and

consequently, the typical transmembrane helical torsion angles displayconsequently, the typical transmembrane helical torsion angles display

far less scatter than in water soluble proteins.far less scatter than in water soluble proteins.

2.2. The lack of scatter is due to the unique amino acid composition and theThe lack of scatter is due to the unique amino acid composition and the

unique membrane environment where water is scarce and hydrogenunique membrane environment where water is scarce and hydrogen

bonds are strong.bonds are strong.

3.3. The scatter due to chemical shiftThe scatter due to chemical shift tensor element magnitude andtensor element magnitude and

orientation variation is almost insignificant.orientation variation is almost insignificant. Indeed, the scatter isIndeed, the scatter is

structurally insignificant compared to structural resolution achieved bystructurally insignificant compared to structural resolution achieved by

other techniques.other techniques.

4.4. Oh yes, PISA wheels do provide a preliminary assessment for the helicalOh yes, PISA wheels do provide a preliminary assessment for the helical

tilt and rotation including which end of an tilt and rotation including which end of an amphipathic amphipathic helix ishelix is

protruding from the bilayer.protruding from the bilayer.

Page 41: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Structural Characterization: The Challenge of Using

Precise Structural Restraints for an Initial Structure

1.1. Orientational Orientational Restraints from uniformly aligned samples areRestraints from uniformly aligned samples are

high precision data with error bars of a few degrees at most.high precision data with error bars of a few degrees at most.

To access these restraints, assignments are needed.To access these restraints, assignments are needed.

2.2. The sign and even magnitude of the dipolar coupling can leadThe sign and even magnitude of the dipolar coupling can lead

to degenerate solutions. Many of these to degenerate solutions. Many of these degeneracies degeneracies areare

resolved by PISA wheelsresolved by PISA wheels

3.3. The The orientational orientational restraints result in degenerate structuralrestraints result in degenerate structural

solutions, such as the solutions, such as the orientational orientational restraints used in solutionrestraints used in solution

NMR. Many of these NMR. Many of these degeneracies degeneracies are resolved by PISAare resolved by PISA

wheels.wheels.

4.4. The overall problem is a conformational space separated byThe overall problem is a conformational space separated by

high energy barriershigh energy barriers

Page 42: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Spectra of M2 22-62

Three samples1) 15N Leu2) 15N Val3) 15N Phe

SSDPLVVAA30SIIGILHLIL40WILDRLFFKS50IYRFFEHGLK60RG

»» Val27 and Val28 represent absolute assignments as does Leu59

Mukesh Sharma

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Spectra of M2 22-62

For reference Val spectrumis shown.

Ile spectrum results inabsolute assignments forIle33 and Ile 51

Two samples were preparedfrom UL 15N media:1) including naturalabundance Leu, Ala, Phe,Val, Gly & Ile - magenta2) including naturalabundance Leu, Ala, Phe,Tyr, Val & Ile - red

Mukesh Sharma

SSDPLVVAA30SIIGILHLIL40WILDRLFFKS50IYRFFEHGLK60RG

Page 44: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

Degeneracies in observing the dipolar couplings

• Outlined in Black is the PISEMA powder pattern correlating the Chemicalshift tensor with the dipolar tensor

• Note that the Clear space marked A can be assigned a positive dipolarcoupling, while the space, C is assigned a negative coupling. B isambiguous.

• However, for resonances on the surface of a PISA the sign can bepredicted, based on the position on the wheel. Only for a wheelprecisely at a tilt angle of 58° is the sign of the coupling ambiguous.

»» consequently

these degeneracies

associated with

the dipolar

interaction are

eliminated

Page 45: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

PIPATH : Graph Theory Based Assignment Protocol

of PISEMA class Spectra for Helical Proteins.

!"#$%&'()'*+',-.'/0112'3

• This program works in $,% space to

achieve the sequence specific

assignments. Torsion angles can be

assigned to any pair of peptide planes

characterized by the PISEMA data

set.

• In doing so it searches for the

assignments that achieves an

assignment set that is most consistent

with the helix characterized by the

PISA wheel.

»» Consequently, in finding the assignment solution this program also finds an

initial structural solution. In finding several good fits the program finds a set of

initial structures.

Page 46: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

PIPATH : Graph Theory Based Assignment Protocol

of PISEMA class Spectra for Helical Proteins.

!"#$%&'()'*+',-.'/0112'3

• PIPATH in using graph theory

efficiently searches all

combinations of possible

assignments

• The number of potential solutions

is huge, but the number of

olutions consistent with the

PISA wheel analysis are very

limited and form a tight bundle

of possible solutions

Page 47: From PISA Wheels to High Resolution Protein Structurefbml.scripts.mit.edu/Downloads/Cross_L1.pdfWang et al., (2000) J. Magn. Reson. 144:162 Structure Determination from Aligned Samples

PIPATH : Graph Theory Based Assignment Protocol

of PISEMA type Spectra for Helical Proteins.

PIPATH transforms the assignment

problem into a path-finding problem.

• N data points can be connected with N-1

edges.

• Each edge relates two data points with a

set of $,% angles.

• Let cost be defined as deviation from

torsion angles for canonical helices.

• The goal is to find a path going through

all the data points once with the least

cost.

!"#$%&'()'*+',-.'/0112'3

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PIPATH : Graph Theory Based Assignment Protocol

of PISEMA type Spectra for Helical Proteins.

• Output of the programs is resonance

assignments and a backbone

structure in PDB format that can be

used as an initial structure for further

refinement.

• Unique structures can be obtained

with few specific labels or

unambiguous assignments.

• PIPATH performance as a function

of peptide length using simulated

data for 62 transmembrane !-helices

from the PDB.

!"#$%&'()'*+',-.'/0112'3

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Fully Assigned using PIPATH

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Determining the Sign of the Cosine for Amphipathic

Helix Tilt

Carbonyls are tilted away

from the Helix axis

Amide N-H groups are tilted

in toward the helix.

A] A Helix with the C-

terminus more buried than

the N-terminus in the

membrane would have N-H

groups closer to the magic

angle for the hydrophobic

residues

B] A Helix with the C-

terminus less buried than

the

N-terminus would have

N-H groups closer to 90°

for the hydrophobic

residues.

Hydrophilic

Hydrophobic

A.

B.

Hydrophobic

Hydrophilic

N

N

C

C

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Spectra of M2 22-62

$ = Tor (u1, u2, u3) = Tor (u1, u2, B0) + Tor (-B0, u2, u3) % = Tor (u2, u3, u4) = Tor (u2, u3, B0) + Tor (-B0, u3, u4

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»» where a and b are unit

vectors representing

bonds, such as N-H and

N-C in the peptide

plane. Cos)ab is a bond

angle and cos* is

derived from the NMR

spectra.

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»» Despite all of these restraints this chriality ambiguity exists. However, for data

in a PISA wheel this ambiguity is readily resolved unless the helix is parallel to

the bilayer normal and Bo - a very rare situation.

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Torsion angles from

PISEMA data

$ = Tor (u1, u2, u3) = Tor (u1, u2, B0) + Tor (-B0, u2, u3) % = Tor (u2, u3, u4) = Tor (u2, u3, B0) + Tor (-B0, u3, u4

The orientation of the unit vectors wrt Bo is

determined from the PISEMA data and the known

covalent geometry.

Assuming that the peptide plane is planar, the torsion

angles can be determined.

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»» Furthermore, the ambiguities or degeneracies that have been described in the

literature for the torsion angles are also eliminated if the degeneracies in the peptide

planes are eliminated. - A unique set of torsion angles results

X

X

X

X

X

X

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Structural Assembly and Refinement Strategy

Structural data is recorded in liquid crystalline lipid bilayers andtherefore it would inappropriate to refine the structure in theabsence of this environment. Therefore, refine with MD:

1) From the NMR restraints develop an initial structure - for the M2project this is a monomeric protein structure. PIPATH followed byNIH-Explor

2) Build a tetrameric initial structure using the initial monomer structureand inter-monomer distances - use NIH - Explor

3) Place tetramer in a pre-equilibrated bilayer with a properlyprotonated histidine tetrad.

4) Run restrained MD at constant pressure, temperature with zerosurface tension and a semi-isotropic boundary condition. Restraintson symmetry and torsion angles were imposed.

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Refinement Strategy - Result of Restrained MD

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Refinement Strategy - Result of the Restrained MD

»» Result of the restrained MD is that the comparison between theexperimental data and predicted values from the refined structureillustrate a good fit.

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»» The overall result is very well defined torsion angles, but note that there is

some scatter in the % torsion angle - similar results were obtained for the $

torsion angle.

From Topology to High Resolution for the

Transmembrane Domain

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Backbone Structure of the Closed

State of the M2 Transmembrane

Domain Characterized by

Orientational and Distance

Restraints - Derived from

Solid-State NMR

A pore exists on the Proton Channel axis formed by this Tetrameric Structure.The Pore is lined with a functionallyImportant tetrad of histidines and Tryptophan sidechains.

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M2 Transmembrane Domain with & without Amantadine

Conggang Li, Jun Hu

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Analyses of the PISEMA Data for M2-TMD

in the Presence of AmantadineJun Hu

Conggang Li

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M2-TMD Structural Comparison

With Amantadine Without Amantadine

Nishimura et al., 2002Hu et al., 2007Amantadine is modeled into this

structure that has been refinedwith MD in a lipid environment.

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Correlation Restraints

Mukesh Sharma

For the refinement of structures using orientational restraints resonancesfrom adjacent peptide planes are utilized, but there is in fact far morerestraints available from the PISA wheel. Next nearest neighborpeptide planes should be separated on the wheel by 200°; residues Iand I+7 should be separated by -20°, etc.

Pept. Plane Ideal Helix Obs. Helix Avg. Rot.26, 27 100° 90° 90°27, 31 400° 365° 91°27, 28 100° 70° 70°27, 34 700° 680° 97°27, 38 1100° 1085° 99°27, 42 1500° 1455° 97°29, 33 400° 415° 104°29, 36 700° 680° 97°29, 40 1100° 1080° 98°29, 43 1400° 1390° 99°33, 34 100° 95° 95°

»» It is clear that the long range correlationswould make a valuable contribution to thecharacterization of the structure. We arecurrently implementing these new restraintsin our structures.

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1H Tensor Characterization

»» Powder Patterns correlating the 1H chemical shifttensor with the 15N chemical shift tensor areobtained with a WIM Hetcor Echo sequence. Asample of microcrystalline 15N alanyl-Leucine wasobserved. Variations in the magnitude of the N-Hdipolar interaction across the powder pattern resultin varying efficiency of the cross polarization andtherefore varying intensity as a function of CP time

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1H Tensor Characterization

»» Tensor Orientation:Tensor Magnitudes: #xx=17, #yy=10.4, #zz=-2

+H=+7°

+H=+7°

+H=-7°

+H=-7°

+H=-7°

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Potential Use of 1H Chemical Shift as Structural Retraints

Prof. Myriam Cotton, Riqiang Fu, Milton Truong

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Conclusions

•• Membrane Proteins requires a structural technology that can observe the Membrane Proteins requires a structural technology that can observe theprotein in an environment that resembles the membrane environment asprotein in an environment that resembles the membrane environment asclosely as possible.closely as possible.

•• The environment The environment dramatically influences the structuredramatically influences the structure

•• PISA wheels provide approximate values for tilt (including the sign of the PISA wheels provide approximate values for tilt (including the sign of the coscos))and rotation ofand rotation of heliceshelices- they define the residues of the helix- they define the residues of the helix- - they define the average torsion angles for the helixthey define the average torsion angles for the helix- they provide correlation restraints- they provide correlation restraints throughout the entire helixthroughout the entire helix

•• PISEMA data provides high resolution structural restraints leading to high PISEMA data provides high resolution structural restraints leading to highresolution backbone structuresresolution backbone structures

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FSU Chem & Biochem

Mukesh Sharma Milton Truong

Dylan Murray Nabanita Das

Thach Can Anna Kozlova

Huajun Qin Dr. Sorin Luca

Dr. Da Qun Ni

Dr. Frantz Jean-Francois

FSU Mathematics

Prof. Jack Quine

Prof. Richard Bertram

FSU Physics

Myunggi Yi

Prof. Huan-Xiang Zhou

NHMFL

Dr. Riqiang Fu

Dr. William Brey

Peter Gor’kov

Brigham Young Univ.

Prof. David Busath

Hamilton College

Prof. Myriam Cotten

The NHMFL:

A National User Facility