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2. BIOL2012- Exploring Proteins Structure and Function > JW - Protein Architecture II > Flashcards

JW - Protein Architecture II Flashcards

1
Q

What is the typical structure of most globular proteins?

A

Most globular proteins have a domain structure

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2
Q

How many domains are present in the cell surface protein CD4?

A

4 IG domains

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3
Q

What is an example of a conserved domain?

A

EGF

  • Conserved in many different protein structures (Neu, EGF precursor and TPA)
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4
Q

How are domains identified?

A

Using amino acid sequence profiles

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5
Q

Domain vs Module vs Repeat

A

Domain: a folded structural unit; the sequence need not be contiguous

  • e.g. MHC II

Module: a domain with a contiguous sequence, repeatedly used in diverse proteins

  • e.g. F3

Repeat: a unit that does not fold in isolation; several copies are needed

  • e.g. Leu-rich repeat
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6
Q

What are some examples of popular protein domains? (7)

A
  • IG
  • F3
  • F1
  • EGF
  • SH2
  • SH3
  • Kinase domain
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7
Q

What are antibodies made from?

A

IG domains

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8
Q

Describe the structure of IG domains (2)

A

IG domain:

  • Around 100 residues
  • 2 layered sandwich of 7( to 9) anti parallel b-strands, in two b-sheets with Greek key motif
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9
Q

What are the 2 main variants present in IG domains?

A

C1 variant:

  • 4 stranded b-sheet DEBA & 3 stranded b-sheet GFC

C2 variant:

  • 3 stranded b-sheet EBA & 4 stranded b-sheet GFCC’
  • C’ strand switched sheet with respect to C1 variant
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10
Q

What is the function and structure of the MHC class I protein?

A

Function:

  • presents antigens (peptides 8-10 residues) to T lymphocytes

Structure:

  • non-covalent heterodimer
  • a-chain: contains a3-domain and peptide binding domain
  • b-chain: b2m (single IG-domain)

Two IG domains: a3 and b2m

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11
Q

What is Titin?

A

Giant muscle protein

  • 90% IG or IG-like domains
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12
Q

What do interdomain linkers act as?

A

Hinges

  • Passive elements that flexibly connect the functional domains
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13
Q

What do unstructured protein regions contain?

A

Binding motifs

  • short and unstructured
  • multiple specific protein binding motifs
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14
Q

What are Integrins?

A

Family of cell adhesion receptors, bind to extracellular matrix components

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15
Q

What are
Intrinsically Disordered Proteins (IDP) and what are their features? (2)

A

Parts of protein sequences or entire proteins that lack a defined 3D structure

  • They may be entirely random coil or partially structured
  • They carry out their function as unstructured proteins
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16
Q

What are 2 prominent examples of IDPs?

A

a-synuclein: human 140aa, functions in synaptic transmission

different structural features depending on environment:

  • lipid bound
  • Tetramer
  • beta rich
  • fibrilar state

Tau(s): stabilizes microtubules, phosphorylation state disease related

17
Q

What is an example of a protein that contains both folded domains and unstructured regions?

A

P53: tumor suppressor protein contains both folded domains and IDPs

IDPs:

  • TAD1 transactivation region
  • PRR proline rich
  • TD tetramerisaion region
  • RD regulatory region
18
Q

How do we study primary, secondary and tertiary structures of proteins?

A

1) Primary Structure

Chemically; Edman degradation

  • Sequence of amino acids

Mass spectrometry

  • Identification of protein fragments

2) Secondary and tertiary structures

  • There is an array of methods available
19
Q

What is a formula involed in a spectroscopic method for determining protein structure?

A

Beer-Lambert Law

A = e l c

e: molar extinction coefficient
l: path length in cuvette
c: concentration of protein (DNA,…)

20
Q

What is Circular Dichromism (CD)?

A

CD is the unequal absorption of left-handed and right-handed circularly polarized light

  • In proteins, the peptide bond is an optically active group giving rise to circular dichroism which in turn is sensitive to protein conformation

Helps determine secondary structure of a protein

21
Q

Features of Electron Microscopy ? (5)

A
  • Images of single particles is possible (limit resolution ~20A)
  • Averaging or crystalline samples resolution ~4A) needs extensive image processing
  • Routine use of EM on “ metal stained” samples for increased contrast
  • Without metal stain but sample freezing leeds to fewer artefacts
  • Whole cells can be imaged and distribution of proteins analysed inside the cell
22
Q

What are 2 major limitations of Electron Microscopy?

A
  • Radiation damage
  • In transmission EM very thin samples needed
    (~<500nm)

2. BIOL2012- Exploring Proteins Structure and Function (22 decks)

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