Major Types of Association of Proteins with Cell Membranes From Alberts et al
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
Common Non-Charged Amino Acids From Cooper
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
Amino Acid Codes
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
Ionization of Amino Acid Ionization of glycine Hames & Hooper, Biochemistry (2000)
pk Values and Molecular Weights of Amino Acids Hames & Hooper, Biochemistry (2000)
Proteins Are Polymers of Amino Acids Structural picture of polypeptide ψ φ Ramachandran plot [Branden & Tooze]
Two Polymer Languages of Biology Phillips et al., Physical Biology of the Cell (2009)
Nucleotides and DNA A: adenine; T: thymine; G: guanine; C: cytosine
Genetic Code A: adenine C: cytosine G: guanine U: uracil
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
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
Typical Alpha-Helical and Beta-Barrel Proteins BtuCD Vitamin B12 Transporter FecA Ferric Citrate Uptake Receptor From Walian et al., Genome Biology (2004)
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
Deviations From the Classical Alpha-Helix: Alpha-II Hydrogen bonds N -> N+4 Alpha-I Alpha-II From Krimm et al
Deviations From the Classical Alpha-helix: pibulges Hydrogen bonds N -> N+5 From Popot and Engleman
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
Deviations From the Classical Alpha-helix: Proline Bends or Kinks From Popot et al
Atypical Collagen Helices From Cooper From Alberts et al
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
Na+/H+ Antiporter: An Example of Tilted and Broken Transmembrane Helices From Hunte et al
Glutamate Transporter: Reentrant Loops and Broken Helices From Elofsson et al
Relative Propensity of Amino Acids to Form Alpha-Helices Ala: 1.489 Arg: 1.224 Asn: 0.772 Asp: 0.924 Cys: 0.966 Gln: 1.164 Glu: 1.504 Gly: 0.510 His: 1.003 Ile: 1.003 Leu: 1.236 Lys: 1.172 Met: 1.363 Phe: 1.195 Pro: 0.492 Ser: 0.739 Thr: 0.785 Trp: 1.090 Tyr: 0.787 Val: 0.990 From Deleage and Roux Gly and Pro are often called helix-breakers (Pro kinks and Gly hinges)
Helix-Coil Transition From Eaton et al
The Beta-sheets (can be parallel or anti-parallel) From Lodish et al
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)]
Typical Architecture of beta-barrels OmpX Contain a lot of aromatic amino acids From Wimley
Alpha and Beta Content is Highly Variable Among Membrane Proteins From Alberts et al
Examples of Known Alpha- Helical Proteins Often contain helical dimers or helical bundles From Popot et al
Examples of Known Beta-Barrel Proteins From Popot et al
More Examples of Beta-Barrel Proteins FepA Maltoporin OmpLA TolC From Wimley Alpha-hemolysin
From Bracey et al A New Structural Class of Membrane Proteins
Glutamate Transporter Another Example of An Unusual Protein Architecture From Yernool et al
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
Lipids Can Mediate Contacts Between Monomers, Helping to Maintain Quaternary Structure Bacteriorhodopsin trimer From Lee KCSA tetramer
Examples of Various Interactions Between Helices: Disulfide Bonds From Cooper
Examples of Various Interactions Between Helices: Hydrogen Bonds (Polar Clamps) From Adamian et al SC side chain/side chain SB side chain/backbone
Examples of Various Interactions Between Helices: Hydrophobic From Alberts et al Formation of a coiled coil
Knob-into-Hole (Ridgeinto-Groove) Packing From White et al Glycophorin dimerization is governed mostly by van der Waals interactions From Popot et al
Organizational Levels of Protein Structure From Alberts et al
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)
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.
Membrane Protein Insertion and Folding From White et al Thermodynamic cycle of a membrane protein
Interactions of Membrane Proteins From White et al
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
Hydropathy Plots Can Predict Protein Transmembrane Regions From Alberts et al
Traditional Amino Acid Hydrophobicity Scale Used to Calculate Hydropathy Plots Ala: 1.800 Arg: -4.500 Asn: -3.500 Asp: -3.500 Cys: 2.500 Gln: -3.500 Glu: -3.500 Gly: -0.400 His: -3.200 Ile: 4.500 Leu: 3.800 Lys: -3.900 Met: 1.900 Phe: 2.800 Pro: -1.600 Ser: -0.800 Thr: -0.700 Trp: -0.900 Tyr: -1.300 Val: 4.200 From Kyte and Doolittle
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
Importance of Taking a Protein Backbone into the Account for Accurate Prediction of the Transmembrane Helices From White et al
The Best Prediction Is Given By the Difference Between the Interfacial and the Hydrophobic Scale RC L-subunit From White et al
Energetic Advantages of the Backbone Hydrogen- Bonding and Interfacial Tryptophans From White et al
From White et al Tryptophans and Tyrosines Are Usually Found at the Membrane Interfaces
Translocon Assisted Protein Insertion From Egea et al From White et al
Translocon Structure From White et al
Protein Sorting By Translocon Secretion Insertion From van den Berg et al
Membrane Protein Translocation in Bacteria From Elofsson et al
The Sorting Is Based on Hydrophobicity From Hessa et al
Positional Effects in the Biological Hydrophobicity Scale From Hessa et al
Energy Profiles Calculated From the Known Membrane Protein Structures From Ulmschneider et al
Alpha-I Geometry Of Beta Sheets Vs. Alpha Helices Beta From Alberts et al