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4 and 5 Flashcards

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1
Q

Proteins

A

linear polymers of alpha-L-amino acids linked via peptide bonds

amino group + carboxyl group

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2
Q

recall on chirality

A

S/L = anti clockwise
R/D = clockwise

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3
Q

Hydrophobic Amino Acids

A

no H-bonds able to form with the side chains
> missing N/O

e.g. Alanine, NH3-C-COOH -H R=CH3

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4
Q

Glycine

A

R=H
smallest amino acid
and is also hydrophobic
and non-chiral

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5
Q

Charged Amino Acids

A

R=COOH or NH2
> COO- or NH3+
(acidic , donates proton
or basic, accepts proton)

e.g. Aspartic acid R=CH2COOH

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6
Q

Polar Amino Acids

A

usually contain: N,O,S (Thiol)
> HB forming

e.g. Serine
R=CH2-OH

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7
Q

Zwitterionic

A

A.A. are Zwiterionic
> 2 diff pk Values

COO- at low pH
NH3+ at high pH

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8
Q

Peptide Bond

A

2 A.A. = O=C-N-H + H2O

metastable
hydrolysis = 10kJ/mol

40% double bond char.
resonance stabilised (mesomerism)
planar

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9
Q

Polypeptide

A

Series of A.A.

Proteins = polypeptides of 40-10,000s of A.A.

Length proportional to organism
e.g. Human proteins are on avrg larger than E.coli

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10
Q

Why does protein cut off at 10,000 AA Polypeptides

A

Only certain length of polypeptides can adopt the 3D folded structure that is typical of proteins

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11
Q

Average MW of eukaryotic protein

A

110Da/AA
50kDa = average mw.

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12
Q

Covalent interactions in Proteins

A

defined by bond lengths and bond angles in AA / Peptide bond

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13
Q

Common Bond lengths

A

C-C = 1.54 Ang.

C=C is less than C-C (change by 0.2)
C=O is less than C-O

C-C<C-N<-C-O<C-H (change by 0.05 for first 3 at least)

C-H = 1.05 Ang.

change by 0.1 Ang = 20kJ/mol

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14
Q

Bond angles determined by

A

Orbital geometry of central atom / Hybridisation

CH4 = Sp3
CH2=CH2= Sp2

change by 5 degrees = 1.3kJ/mol
> less than for change in bond length
> therefore less tightly defined than bond length

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15
Q

Rotation about C-N peptide bond

A

Hindered
> cis and trans isomer
> high activation energy so it’s slow to conv.

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16
Q

Which peptide bond in proteins?

A

Trans peptide bond in 99.9%
(opp. sides)

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17
Q

Cis peptide bond?

A

in some X-Pro proteins

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18
Q

Protein structure conformations
(two angles to consider)

A

3D structure defined by torsional angle rotations around:
Main chain/backbone
side chain torsions

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19
Q

Torsion Angles basics

A

Staggered or Eclipsed dep. on angle
> staggered = lower energy

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20
Q

what are rotamers?

A

side chain conformational isomers

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21
Q

Torsion angles in polypeptides:

A

Side chain: defined by chi

Main chain:
3 parameters
> N-C-alpha
> Calpha-C
> C-N (usually 180 in trans peptide bond)

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22
Q

Ramachandran Plot

A

due to sterics only certain main chain torsion angle conformations are allowed
> Plots pairs of the 2 parameters (with 3rd as 180) against actual observed protein angles

> shows excluded and preferred regions

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23
Q

Non covalent interactions

A

FORMS 3D STRUCTURE/FOLD of protein !!!

> electrostatic (charged and neutral grps)
h-bonding
hydrophobic effect

= delicate balance between forces
each type may have energies in 1000s but free energy of unfolding is only 0.4kJ/mol
> as they mostly compensate for each other

> multiple protein states at similar energy levels

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24
Q

Non-cov:
Electrostatic interaction of charged groups

A

defined by coulombs law
> distance between two charges
> dielectric constant of MEDIUM
Protein constant = 4 (Vacuum = 1, Water = 80)
vacuum to protein/water = favourable
water to protein/vacuum = unfavourable

Inside protein = no isolated net charges
> complementary charge groups form ion pairs / salt-bridges
»> HOWEVER overall stabilising affect is SMALL
in hydrophobic/burried regions, affect is bigger ofc

Calc. electrostatic is complex
> many charged grps, influence pK, dielectric varies,
» Protein env also dissociation behaviour / ionisation

Most charged groups are solvated on the protein surface
Solvation energy ≈ Energy of interaction → cancels out
Entropic penalty for forming ordered interactions
= minority of ion pairs = desolvated (significant but minor)
= majority = surface + solvated
surface = not well conserved, contribute less

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25
Non-cov interactions: VDW
Electrostatic interaction between neutral grps Dipole-Dipole = Strong London = weak but large = 1/r^6 > interaction prop. to distance > steric repulsion = 1/r^12 = Lennard Jones Potential graph to show optimal distance for vdw contribute to protein stability SIGNIFICANTLY !!
26
Non-cov interactions: Hydrogen Bonding
predom. electrostatic/dipole interactions with 10% cov. char. > closer distance than vdw Donor: Polarised D-H bond Acceptor: partial negative charge and lone e- pair (N/O) H-B energy in proteins = 8-30kJ/mol unfolded protein makes h-bonds with similar enthalpy WITH water > H-bonds to water = disfavoured >> net stabilisation = 2-8kJ/mol Little net stabilisation BUT important for GUIDING FOLDING PATTERNS!!! > H-bonds are DIRECTED / Linear >> dep. on distance AND angle
27
Non-cov interactions: Hydrophobic effect
in water hydrophobic surfaces are covered by CLATHRATE like structures > entropically unfavoured!! >> droplet formation to reduce surface (Solvent accessible area) no change in enthalpy but entropy is increased > dec free energy (prop. to SAA) MAIN DRIVING FORCE OF PROTEIN FOLDING !!
28
Non-cov intereeactions Summary
Electrostatic: structure, function def, modulation of side-chain pK VDW: dense packing of atoms, stability H-Bonds: structure, function def Hydrophobic effect: main determinant of protein stability
29
Protein Structure: Heirarchy
Primary: AA seq Secondary: common structural motifs Tertiary: 3D folding (sec+loops) Quaternary: stable assembly of multiple polypeptide chains
30
Ramachandran Plot
Only subset of mainchain torsional angles in polypeptides is allowed/favoured > favoured regions correspond to common secondary structures Top Left = Beta strands Bottom Left = Right handed a-helix in the top right little part = left handed a-helix (from polyproline and glycine)
31
Protein Secondary structure: Helices Parameters and degenerate examples
Parameters: n - number of peptide/repeating units per turn p - pitch, distance alone one turn r - p/n (rise) degenerate p = 0, ring n = 2, flat ribbon left handed is when n is negative
32
Protein Secondary structure: Helices representation
N(m) helix n = number of residues per turn m = number of atoms, incl H, for closing H-bond (so from C=O to N-H) alpha helix = most common type = 3.6(13) = square shape from top view < 13 = thinner = triangular shape ^^ > 13 = thicker sometimes m = 0 in case of polyproline > not possible to form any H-bonds
33
Alpha helix
favoured mainchain torsion and favourable h-bond pattern > v common > rigid > 4-25 residues typically (avrg 12) aka christmas tree has dipole moment which affects (N = + C = -) >> pK and pref binding sites
34
Helical wheel diagram
Orientation of side chain types in helix can be represented by these > useful to analyse packing
35
B strands and sheets
can be desc as helix with 2 residues per turn > rep as arrow pointing towards C-term > most have a twist for optimal side chain packing > not autonomous >> req. H-bond partner 2-15 strands wide (avrg = 6) > can assemble into MIXED b-sheets > parallel = LESS STABLE; in mixed only account for 20% parallel and antiparallel Beta sheets = PARTNERS >> creating B-pleated sheets
36
Antiparallel B-sheets
Neighbouring B strands run in opposite directions > parallel arrangement of H-bond in main chains > side chain/R alternate in up and down pointing
37
Parallel B-sheets
neighbouring B strands in identical direction > disordered arrangement of H-bond in main chain > side chain/R alternate in up and down pointing (same as anti)
38
Protein Secondary Structure + Loops? + topology diagram ?
chains consist of regular secondary structure elements > primarily alpha helix and b-sheets as well as LOOPS >> longer regions without secondary structure >> found mostly at SURFACE >> common = 2-residue turns between two antiparallel b-sheets to cause chain reversal (with H-bond for inc stability) proteins oft. contain unstructured/dynamic loops > some dont adopt 3D structure > many unfolded only adopt folded upon interaction with partners >> can be rep. in topology diagram
39
Protein Supersecondary structures summary
secondary struc commonly combine in 3D to these e.g. helix-turn-helix motif B-hairpin motif (2 antiparallel b-sheets with turn) greek key motif? idk B-a-B motif (with 2 parallel b-strands)
40
Protein Tertiary Structure
Folding of (super)secondary struc and loops into 3D packing and topology
41
Domain def
smallest repeatable unit of protein tertiary structure > typical 80-250 AA
42
Protein Tertiary Structure: Examples general
Helical Bundle: tight packing of hydrophobic in the core Helical Repeats Alpha-beta folds: e.g. TIM > form active site
43
Protein Tertiary Structure: Examples beta folds
B-barrel: antiparallel strands B-sandwich: used for immunoglobulin fold
44
Multi-domain Proteins (Tertiary)
particular higher eukaryotic proteins can consist of multiple domains > active sites typically within one domain but can also be formed at the domain borders > may have ordered or flexible relative orientations
45
Protein Quaternary Struc. (Oligomers)
protein chains assemble to oligomeric structures. Homo-Oligomer: identical subunits Hetero-Oligomer: non-identical subunit number of subunit given as dimer trimer etc isolated subunit = monomer subunit IN oligomer = protomer
46
Homo-Oligomer Symmetry ?
Desc. with Point symmetry > based on single rotational axis = c2, c3 etc Multiple Intersecting axes > D2 (C2 with intersecting axis)
47
Homo-Oligomers formed via
Isologous Interactions (Identical/Similar) > both promoters use same contact area Heterologous Interactions > two distinct patches/diff regions to mediate interaction
48
Hetero-Oligomers assemble to
Pseudo-sym or assymetric structures
49
Protein Dynamics
folded native state = marginally stable E diff between fold/unfolded = 20-60kJ/mol >> Dynamic ! Global Thermal Motion > continuously diffuse translationally AS A WHOLE Internal Thermal Motion > protein atoms are in constant motion WITHIN PROTEIN relative to each other
50
Translational Diffusion
net mean distance traveled in time D = sqrt (6DT) in CELLS 10x slower than in water!! > rmbr 2 microm in 1s for cell 20microm in 1s for water
51
Rotational Diffusion?
determine probability that molecule is still where it was at t=0 > probability dec with inc time exponentially 1/e = rotational correlation time Tc = Molecular weight/2
52
Internal Thermal Motion
> over wide range of diff time scales > larger atomic group = longer
53
Atomic fluctuations along individual bonds time scale
10 ^-15 to 10 ^-11 = FAST/short
54
Collective fluctuations of groups time scale
10 ^-12 to 10^-3 = SLOW/longer
55
Triggered Conf. change in response to stimulus
very long time scale e.g. for ligand binding
56
things to rmbr for time scales
globular regions slower than atoms burried groups slower than non burried internal side chains slower than surface side chains allosteric transitions VERY slow
57
method for studying struc dynamics of proteins
1. NMR (Ensemble) + good resolution achievable - NOE restricted to < 5Ang (influence of atoms thru space) 2. Hydrogen-Deuterium Exchange (Ensemble) 3. Single molecule fluorescence spectroscopy (single molecule) 4. X-ray crystallography / CryoEM (Snapshots) > freeze after triggering conf change > resolution prop to time req to freeze
58
Isotropic displacement Parameter = Crystallographic B factor + def of isotropic
crystallography based on ensemble > req. model for uncertainty single value aka temperature factor 1 Ang. res: B = 10A^2 Isotropic: assumes atom motion is same in all directions of space
59
Anisotropic displacement parameter diff
3 values for each direction of space
60
Molecular dynamics simulations.. (3)
based on force field descriptions to stimulate n visualise molecular motions virtual solvent boxes comp demanding

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