Major Types of Association of Proteins with Cell Membranes. From Alberts et al

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1 Major Types of Association of Proteins with Cell Membranes From Alberts et al

2 Proteins Are Polymers of Amino Acids Peptide Bond Formation Amino Acid central carbon atom to which are attached amino group carboxyl group side chain 20 different amino acids From Cooper

3 Common Non-Charged Amino Acids From Cooper

4 Common Charged Amino Acids From Cooper Whether a particular side chain is charged or not is determined by its proton affinity, which is often expressed as pka = - log(ka) Proton affinities are greatly dependent on the charge environment and can be different for the same amino acid inside and outside of the membrane Normally, basic amino acids have high pka, and acidic have low pka

5 Amino Acid Codes

6 Characteristics of Amino Acids Important for Understanding Protein Structure and Function Size (Molecular weight and Bulkiness) Hydrophobicity (Polarity) Hydrogen-bonding Ability Charge and Proton Affinity (pka) Propensity to form certain protein structures Flexibility From Decoursey Schematics of a hydrogen bond

7 Ionization of Amino Acid Ionization of glycine Hames & Hooper, Biochemistry (2000)

8 pk Values and Molecular Weights of Amino Acids Hames & Hooper, Biochemistry (2000)

9 Proteins Are Polymers of Amino Acids Structural picture of polypeptide ψ φ Ramachandran plot [Branden & Tooze]

10 Two Polymer Languages of Biology Phillips et al., Physical Biology of the Cell (2009)

11 Nucleotides and DNA A: adenine; T: thymine; G: guanine; C: cytosine

12 Genetic Code A: adenine C: cytosine G: guanine U: uracil

13 Proteins Structure Overview Primary structure: linear sequence of amino acids connected by peptide bonds. Amino acid side chains of various size, polarity, and charge are responsible for uniqueness of each protein From Renninger

14 Proteins Structure Overview From Cooper Secondary structure: conformation of protein backbone stabilized by hydrogen bonds between the backbone atoms. Most common forms are: α-helix, β-sheet, and random coil

15 Typical Alpha-Helical and Beta-Barrel Proteins BtuCD Vitamin B12 Transporter FecA Ferric Citrate Uptake Receptor From Walian et al., Genome Biology (2004)

16 The Alpha-Helices Typical α-helix has 3.6 residues per turn and a pitch (rise per turn) of 0.54 nm Hydrogen bonds N -> N+4 From Lodish et al From Alberts et al

17 Deviations From the Classical Alpha-Helix: Alpha-II Hydrogen bonds N -> N+4 Alpha-I Alpha-II From Krimm et al

18 Deviations From the Classical Alpha-helix: pibulges Hydrogen bonds N -> N+5 From Popot and Engleman

19 Deviations From the Classical Alpha-helix: 3/10 Helices Helical wheel projections From Biron et al Hydrogen bonds N -> N+3 3/10 helix Alpha-I

20 Deviations From the Classical Alpha-helix: Proline Bends or Kinks From Popot et al

21 Atypical Collagen Helices From Cooper From Alberts et al

22 Transmembrane Helices Often, a typical integral protein consists of transmembrane helices, connecting loops (can be in β-turn form), and two tails (C and N) The helices can deviate from the membrane normal Intramembrane parts tend to be hydrophobic From Alberts et al

23 Na+/H+ Antiporter: An Example of Tilted and Broken Transmembrane Helices From Hunte et al

24 Glutamate Transporter: Reentrant Loops and Broken Helices From Elofsson et al

25 Relative Propensity of Amino Acids to Form Alpha-Helices Ala: Arg: Asn: Asp: Cys: Gln: Glu: Gly: His: Ile: Leu: Lys: Met: Phe: Pro: Ser: Thr: Trp: Tyr: Val: From Deleage and Roux Gly and Pro are often called helix-breakers (Pro kinks and Gly hinges)

26 Helix-Coil Transition From Eaton et al

27 The Beta-sheets (can be parallel or anti-parallel) From Lodish et al

28 LARGE RANGE OF LENGTH SCALES properties depend on length scale of measurement complex, hierarchical structure processing is the key [P. Ball, Made to Measure (1997)]

29 Typical Architecture of beta-barrels OmpX Contain a lot of aromatic amino acids From Wimley

30 Alpha and Beta Content is Highly Variable Among Membrane Proteins From Alberts et al

31 Examples of Known Alpha- Helical Proteins Often contain helical dimers or helical bundles From Popot et al

32 Examples of Known Beta-Barrel Proteins From Popot et al

33 More Examples of Beta-Barrel Proteins FepA Maltoporin OmpLA TolC From Wimley Alpha-hemolysin

34 From Bracey et al A New Structural Class of Membrane Proteins

35 Glutamate Transporter Another Example of An Unusual Protein Architecture From Yernool et al

36 Proteins Structure Overview Tertiary structure: arrangement of protein helices and loops stabilized by interactions of amino acid side chains with each other, with the backbone, and with lipids. Interactions of side chains include electrostatic (charge-charge), hydrogen-bonds, disulfide bonds, van der Waals, and hydrophobic interactions Quaternary structure: arrangement of individual protein monomers (subunits) into oligomers (can be homo- or hetero-, and di-, tri-, tetra-, etc.) Linderstrøm-Lang

37 Lipids Can Mediate Contacts Between Monomers, Helping to Maintain Quaternary Structure Bacteriorhodopsin trimer From Lee KCSA tetramer

38 Examples of Various Interactions Between Helices: Disulfide Bonds From Cooper

39 Examples of Various Interactions Between Helices: Hydrogen Bonds (Polar Clamps) From Adamian et al SC side chain/side chain SB side chain/backbone

40 Examples of Various Interactions Between Helices: Hydrophobic From Alberts et al Formation of a coiled coil

41 Knob-into-Hole (Ridgeinto-Groove) Packing From White et al Glycophorin dimerization is governed mostly by van der Waals interactions From Popot et al

42 Organizational Levels of Protein Structure From Alberts et al

43 Protein Domains From Ponting et al Domains within protein structures are usually defined as spatially distinct structures that could conceivably fold and function in isolation (Ponting et al)

44 Protein Motifs and Folds Motif (or supersecondary structure) is a combination of secondary structures that has a particular topology and is organized into a characteristic three-dimensional structure (e.g., coiled-coil motif or helix-loop-helix motif). It can be smaller or equal to a domain. Sometimes, motif is understood simply as a short conserved amino acid pattern. The core 3-D structure (or a topology) of a protein is called a fold. It can be larger or equal to a domain. Major classes of the folds: all-alpha, all-beta, alpha/beta (beta-alpha-beta units), alpha+beta (segregated alpha and beta regions), multidomain.

45 Membrane Protein Insertion and Folding From White et al Thermodynamic cycle of a membrane protein

46 Interactions of Membrane Proteins From White et al

47 Are Membrane Proteins Inside-Out Proteins? Controversial theory of membrane proteins being inside-out proteins as opposed to soluble proteins. It was claimed that soluble (globular) proteins have hydrophobic residues inside and hydrophilic outside, and membrane proteins have it vice versa, namely hydrophobic residues facing lipids, and hydrophilic facing the inside. Analysis of larger number of available membrane protein structures showed that this is not quite true, as van der Waals interactions between the helices play very important role

48 Hydropathy Plots Can Predict Protein Transmembrane Regions From Alberts et al

49 Traditional Amino Acid Hydrophobicity Scale Used to Calculate Hydropathy Plots Ala: Arg: Asn: Asp: Cys: Gln: Glu: Gly: His: Ile: Leu: Lys: Met: Phe: Pro: Ser: Thr: Trp: Tyr: Val: From Kyte and Doolittle

50 The Improved Hydrophobicity Scale Takes Backbone and Interfacial Effects into the Account More important considerations: protonation states of potentially charged residues, and charge pairs From White et al

51 Importance of Taking a Protein Backbone into the Account for Accurate Prediction of the Transmembrane Helices From White et al

52 The Best Prediction Is Given By the Difference Between the Interfacial and the Hydrophobic Scale RC L-subunit From White et al

53 Energetic Advantages of the Backbone Hydrogen- Bonding and Interfacial Tryptophans From White et al

54 From White et al Tryptophans and Tyrosines Are Usually Found at the Membrane Interfaces

55 Translocon Assisted Protein Insertion From Egea et al From White et al

56 Translocon Structure From White et al

57 Protein Sorting By Translocon Secretion Insertion From van den Berg et al

58 Membrane Protein Translocation in Bacteria From Elofsson et al

59 The Sorting Is Based on Hydrophobicity From Hessa et al

60 Positional Effects in the Biological Hydrophobicity Scale From Hessa et al

61 Energy Profiles Calculated From the Known Membrane Protein Structures From Ulmschneider et al

62 Alpha-I Geometry Of Beta Sheets Vs. Alpha Helices Beta From Alberts et al