CHEM 3310H Lecture 18 - Protein Chemistry and Enzymology PDF

CHEM-BIOL 3310H Protein Chemistry and Enzymology Lecture 18: Quaternary Structure & Oligomeric Proteins References: Getting started with Structural Symmetry and Protein Function.pdf Goodsell & Olson, Structural Symmetry & Protein Function.pdf Various structural files viewable in PyMOL The lecture...

CHEM-BIOL 3310H Protein Chemistry and Enzymology Lecture 18: Quaternary Structure & Oligomeric Proteins References: Getting started with Structural Symmetry and Protein Function.pdf Goodsell & Olson, Structural Symmetry & Protein Function.pdf Various structural files viewable in PyMOL The lecture notes in this file, and the pdf “Getting started with Structural Symmetry and Protein Function” are to be read before you tackle the pertinent sections of the review article by Goodsell and Olson The structure shown on the left is the iron storage protein ferritin, which has 24 subunits arranged in a shell around an iron oxide core. One subunit has been removed to reveal the hollow inside, where the iron oxide core residues. 1  Quaternary structure Quaternary structure is the association of two or more protein chains to form an oligomeric protein (oligo = several, as in several chains). If the chains are identical the protein is a homo-oligomer. If the chains are different, the protein is a hetero-oligomer. Alkaline phosphatase, a homodimeric enzyme The two identical subunits of the alkaline phosphatase dimer are coloured in cyan and pale cyan. 2  Shorthand for describing quaternary structure Lower case Greek symbols denote different protein chains, also called subunits. Subscripts indicate the number of these subunits Brackets indicate how the different subunits may associate. Alkaline phosphatase Hemoglobin α2 quaternary structure (αβ)2 quaternary structure On the left, alkaline phosphatase is a protein with two identical subunits (one shaded in cyan, the other in pale cyan). Another way of saying this that it is a homodimer, and an ever shorter way of expressing this is that it has an α2 structure. On the right, hemoglobin has four chains, making it a tetramer. The subunits are not identical (they differ in their amino acid sequences), which further makes it a heterotetramer. This heterotetramer consists of two different types of subunits, α and β. One α subunit associates with a β subunit, and two of these pairs further associate to form the hemoglobin tetramer. The shorthand way of expressing this is to say that hemoglobin has an (αβ)2 structure. (In the hemoglobin structure the two alpha subunits are in cyan and pale cyan, and the two beta subunits are in yellow and pale yellow. 3  Are there any new interactions to consider? Thankfully, No! Quaternary structure is stabilized by the same interactions that drive protein folding The covalent and noncovalent interactions that you have seen up to this point that describe the folding of a protein chain also apply to proteins with quaternary structure. In many cases the hydrophobic effect contributes to oligomer formation as the contact surface between subunits is rich in nonpolar residues. 4  Examples of closed quaternary structures Dimer Hexamer Tetramer Trimer Closed quaternary structures have a defined limit to the number of subunits present. Octamer 5  Cyclic symmetry in oligomeric proteins Cyclic groups (Cn) are those oligomers that have one axis of symmetry This homodimer belongs to the C2 symmetry group This homotrimer belongs to the C3 symmetry group We are mainly concerned with the point group symmetries that involve axes of rotation (Goodsell and Olson mention a few others but these will not concern us). In the homodimer and the homotrimer shown above the identical subunits within each structure are coloured differently for ease of viewing. The axis of symmetry in each case is at right angles to the plane of the page and is directed towards you, the viewer. This is indicated by the curved arrows at the center of each structure. An oligomer with C2 symmetry, which is common for homodimers, takes two half turns to bring the structure to the same view that you started with, while an oligomer with C3 symmetry takes three 120 degree turns to bring it back to the same view you started with. 6  Dihedral symmetry in protein oligomers C2 C2 C3 This homohexamer belongs to the D3 symmetry group C2 Dihedral groups (Dn) are those oligomers that have a Cn axis of symmetry and n C2 axes of symmetry perpendicular to this. They are often seen in oligomers that have a “back to back” arrangement. The example above is a homohexamer that belongs to the D3 symmetry group. (The structure shown consists of the six catalytic subunits of the enzyme aspartate transcarbamoylase, 1pg5.pdb) The three closet subunits to you are shaded green, cyan, and yellow; behind these are three more in lighter shades of these colors. The C3 axis (pink) projects towards you as on the previous slide, and the three C2 axes lie in the plane of the slide as indicated by the lines. As this is hard to render in two dimensions, refer to the file D3 symmetry.pse which is viewable in PyMOL. The lecture recording that accompanies these notes will also show it. 7  D3_symmetry movie A movie of a molecule with D3 symmetry has been posted to the lecture folder on Blackboard. A structural file viewable in PyMOL has also been posted. 8  For more on symmetry in protein oligomers Read the pdf “Getting started with Structural Symmetry and Protein Function” Use PyMOL to view these structures – C6_symmetry.pse – D3_symmetry.pse – Symmetry_X.pse (this is a homo-oligomer, in which each subunit is identical, but colored differently for ease of viewing. Can you identify which symmetry group it belongs to? 9 Oligomeric proteins can have machine-like properties DNA polymerase delta processivity factor is part of the replication complex. It is a sliding clamp that moves along DNA during its replication. 10  Some oligomeric proteins serve as containers Norwalk virus capsid Mammalian ferritin (a homo-oligomer of 24 subunits) (a homo-oligomer of 180 subunits) Left = the Norwalk virus capsid (www.rcsb.org) ; right, the iron storage protein ferritin; one subunit has been hidden in the ferritin structure to reveal the hollow core. Both have an oligomeric protein shell of cubic symmetry (multiple rotational axes of symmetry). The virus capsid encloses viral DNA, while ferritin can store up to 4500 iron atoms as an iron oxide complex. These are not drawn to scale, as ferritin is much smaller than a virus capsid. 11  ferritin movie A movie of ferritin showing it from different perspectives has been posted to the lecture folder on Blackboard. 12  Heterooligomeric proteins are also common Mitochondrial inner membrane ATP synthase has seven different types of protein chains, with several of these in multiple copies. The blue-purple subunits form a proton-driven motor that powers the red subunits to synthesize the energy currency ATP 13  Open oligomers α-tubulin β-tubulin The protist Giardia intestinalis (Tubulin chains in red) Open oligomers can be extended indefinitely, in principle. The repeat unit of tubulin is a heterodimer of alpha and beta subunits that self- associates to form long chains as part of the cytoskeleton. 14  Advantages of Quaternary Interactions: Stability Alkaline phosphatase Association of two or more chains reduces the of surface area to volume ratio of the oligomer. For example, the alkaline phosphatase monomer unfolds at 43°C, while the dimer can be taken to near- boiling temperatures (97°C) 15  Advantages of Quaternary Interactions: Genetic economy and efficiency Vibrio cholera Type II Secretion System Channel Membrane For some functions, large proteins (>1000 residues) are needed. Transcription and translation are not perfect, and sometimes protein chains will have sequence errors in them – some of which may wreck its function. Which is genetically more robust – one big protein or one built of smaller subunits? 16  Advantages of Quaternary Interactions: Cooperativity Hemoglobin Hemoglobin has four subunits and four oxygen binding sites. O2 binding to one site causes conformational changes that induce the remaining binding sites to increase their affinity for oxygen. This allows hemoglobin to pick up O2 efficiently in the lungs, and release it in the tissues where it is needed. 17 P1: FDS April 20, 2000 11:37 Annual Reviews AR098-05 P1: FDS Now, you are ready! Annu. Rev. Biophys. Biomol. Struct. 2000. 29:105–53 Copyright ! c 2000 by Annual Reviews. All rights reserved April 20, 2000 11:37 Annual Reviews AR098-05 STRUCTURAL SYMMETRY AND PROTEIN Annu. Rev. Biophys. Biomol. Struct. 2000. 29:105–53 FUNCTION Copyright ! c 2000 by Annual Reviews. All rights reserved ?? David S. Goodsell and Arthur J. Olson STRUCTURAL SYMMETRY PROTEIN Annu. Rev. Biophys. Biomol. Struct. 2000.29:105-153. Downloaded from www.annualreviews.org Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037;AND e-mail: [email protected], [email protected] FUNCTION Note: we will not be reading the entire review; you are Access provided by Trent University on 09/17/20. For personal use only. Key Words oligomeric proteins, protein symmetry, protein structure/function responsible only for the following sections: relationships Introduction David S. Goodsell and Arthur J. Olson Annu. Rev. Biophys. Biomol. Struct. 2000.29:105-153. Downloaded from www.annualreviews.org Department of Molecular Abstract The majority of soluble and membrane-bound proteinsBiology, Scripps in modern cellsResearch Institute, La Jolla, California 92037; oligomeric are symmetrical The Symmetry complexesofwith Oligomeric e-mail: moreProteins two [email protected], subunits. [email protected] evolution- ary selection of symmetrical Why Build Symmetrical oligomeric complexes Proteins? is driven by functional, genetic, Symmetry and physicochemical needs. Largeandproteins Cooperativity are selected for specific morphological Access provided by Trent University on 09/17/20. For personal use only. Key Words functions, such as formation of rings, containers, oligomeric and filaments, proteins, and for protein symmetry, protein structure/function cooperative Morphological Functions of relationships functions, such as allosteric regulation and multivalent Symmetry binding. Large proteins are also more stable againstYou do notand denaturation have haveto read areduced the sections surface Abstract Thearea beyond exposed majority of to these. solvent soluble and membrane-bound proteins in modern cells when compared with many individual, smaller areproteins. Largeoligomeric symmetrical proteins arecomplexes constructedwith two or more subunits. The evolution- as oligomers for reasons of error control in synthesis, coding ary selection of efficiency, symmetrical andoligomeric regulation complexes is driven by functional, genetic, of assembly. Symmetrical oligomers are favored because of stability and physicochemical needs. andLarge finite proteins con- are selected for specific morphological trol of assembly. Several functions limit symmetry, functions, such suchas as interaction formationwith DNA containers, of rings, or and filaments, and for cooperative membranes, and directional motion. Symmetry is broken functions, suchorasmodified allostericinregulation many forms: and multivalent binding. Large proteins are also quasisymmetry, in which identical subunits adopt more similar but different stable against conformations; denaturation and have a reduced surface area exposed to solvent You now have enough pleomorphism, in whichto make identical a good subunits form start whendifferent compared on complexes; with manythe paper. pseudosymme- individual, smallerThere mayproteins proteins. Large be sections are constructed that are unclear to you, but we can as talk try, in which different molecules form approximately symmetry mismatch, in which oligomers ofof oligomers different about symmetrical for reasons symmetries these of error during complexes; interact control along their the next few lectures. andin synthesis, coding efficiency, and regulation assembly. Symmetrical oligomers are favored because of stability and finite con- respective symmetry axes. Asymmetry is also trolobserved at several of assembly. Several levels. Nearly functions all symmetry, such as interaction with DNA or limit complexes show local asymmetry at the level of side chain membranes, conformation. and directional Several motion. Symmetry is broken or modified in many forms: complexes have reciprocating mechanisms in which the complex quasisymmetry, in whichis asymmetric, but, adopt similar but different conformations; identical subunits over time, all subunits cycle through the samepleomorphism, set of conformations. in which Global asymmetry identical subunits form different complexes; pseudosymme- is only rarely observed. Evolution of oligomeric try, incomplexes may favor which different the formation molecules form approximately symmetrical complexes; and of dimers over complexes with higher cyclicsymmetry symmetry,mismatch, through ain mechanism of pre- of different symmetries interact along their which oligomers positioned pairs of interacting residues. However, examples have been respective symmetry axes. Asymmetry found for allis also observed at several levels. Nearly all of the crystallographic point groups, demonstrating complexes thatshow functional local need can drive asymmetry at the the level of side chain conformation. Several evolution of any symmetry. complexes have reciprocating mechanisms in which the complex is asymmetric, but, over time, all subunits cycle through the same set of conformations. Global asymmetry is only rarely observed. Evolution of oligomeric complexes may favor the formation CONTENTS of dimers over complexes with higher cyclic symmetry, through a mechanism of pre- INTRODUCTION....................positioned........ pairs.....of..interacting.........residues..... 106However, examples have been found for all THE SYMMETRY OF OLIGOMERIC PROTEINS of the.crystallographic.............point....groups,...... demonstrating 107 that functional need can drive the Characteristics and Natural Occurrence of SymmetryevolutionGroupsof any symmetry................ 108 1056-8700/00/0610-0105$14.00 105 CONTENTS INTRODUCTION................................................ 106 THE SYMMETRY OF OLIGOMERIC PROTEINS........................ 107 Characteristics and Natural Occurrence of Symmetry Groups............... 108 1056-8700/00/0610-0105$14.00 105 18