Understanding Protein Structures: Primary, Secondary, Tertiary, and Quaternary, Slides of Biochemistry

Download Understanding Protein Structures: Primary, Secondary, Tertiary, and Quaternary and more Slides Biochemistry in PDF only on Docsity! PROTEINS Section 2 Molecular YY Structures of SA Proteins • Proteins are composed of AAs. • Distinctive properties of proteins are determined by AA compositions, AA sequences as well as the relative positions of AAs in space. • Proteins need well defined structures to function properly. Their structures are organized in a hierarchy format, that is, primary, secondary, tertiary and quaternary structure. Overview docsity.com § 2.2 Secondary Structure The secondary structure of a protein is defined as a local spatial structure of a certain peptide segment, that is, the relative positions of backbone atoms of this peptide segment. ra ER a Ea Ee meee ee Hee er pee R, H R, H R, H R, H R, 0 Amino-terminal residue Carboxyl-terminal residue docsity.com Repeating units of N(‐H), C, and C(=O)  constitute the backbone.  H‐bonds are responsible for stabilizing the  secondary structure.   The side chains are not considered.   ‐helix ‐pleated sheet ‐turn (‐bend)  random coil  docsity.com Peptide unit • Six atoms, C-C(=O)-N(-H)-C, constitute a planer peptide unit. • The peptide unit is rigid due to the partial double bond property. • C=O and N-H groups are in trans conformation and cannot rotate around the peptide bond. docsity.com “Beads on a string” N-terminus C Peptide unit Backbone C-terminus docsity.com Linus Carl Pauling b. 1901, d. 1994 California Institute of Technology, CA The Nobel Prize in Chemistry (1954), “for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances” The Nobel Peace Prize (1962) docsity.com • A helical conformation is right-handed. • 3.6 AAs per turn and a 0.15 nm vertical distance, creating a pitch of 0.54 nm. • Side chains of AA residues protrude outward from the helical backbone. • The hydrogen-bonds are parallel to the helical axis. §2.2.a -helix docsity.com docsity.com 第n个肽键的O原子 第n＋3个肽键的H原子 0.54 nm 3.6 个残基 0.5 nm 肽链走向 （a） （b） C原子 O原子 N原子 H原子 docsity.com The -CO group of residue n is H-bonded to the - NH group of residue (n+4). ® docsity.com docsity.com • One -turn involves four AAs. The -CO and -NH groups of the first AA are hydrogen bonded to the -NH and -CO groups of the fourth AA, respectively. • The -turn reverses abruptly the direction of a protein backbone. • H-bonds are perpendicular to the protein backbone. §2.2.c -turn docsity.com docsity.com (c) Coiled coil motif (a) Helix-loop-helix motif (b) Zine-finger motif N Consensus sequence: FIV= Gas C sons BY wwcce ose H---H- c Consensus sequence: D/N - DIN - DINIS - [backbone O] - - - - L/D Heptad repeat: [V/N/M] - - L- - - 3 docsity.com §2.2.f Side chains effect • Shape: Pro having a rigid ring (– helix disrupter) • Size: -sheet needs AAs of small side chain. Leu, Ile, Trp, and Asn having bulky sides (hard to form –helix) • Charge: Too many charged AAs in a short region of one peptide is hard to form –helix. docsity.com §2.3 Tertiary Structure The tertiary structure is defined as the spatial  positions of all atoms of a protein, i.e., the  three‐dimensional (3D) arrangement of all  atoms.  docsity.com • A charged group is able to attract another group of opposite charges. • The force is determined by Coulomb’s law. §2.3.b Ionic interaction docsity.com § 2.3.c Hydrogen bond A hydrogen atom is shared by two other atoms. H-donor: the atom to which H atom is more tightly attached, and the other is H-acceptor. Hydrogen Hydrogen Hydrogen Hydrogen donor acceptor donor acceptor ee = ee SSS a 2.88 A 3.04 A ® docsity.com • An asymmetric electronic charge around an atom causes a similar asymmetry around its neighboring atoms. • The attraction between a pair of atoms increases as they come closer, until they are repelled by van der Waals contact distance. §2.3.d van der Waals force docsity.com Ribonuclease A pancreatic enzyme that hydrolyzes RNA 124 AAs Mainly B-sheet Highly compact and nonpolar interior 4 disulfide bonds docsity.com Rhodopsin Photoreceptor  protein 7 trans‐membrane  helices 11‐cis‐retinal  chromophore in  the pocket Residues are  modified. docsity.com §2.3.e Domain Large polypeptides may be organized into structurally close but functionally independent units. Fiberousis protein docsity.com • Reversibly bind to the hydrophobic portions to advance the formation of correct peptide conformations • Bind to misfolded peptides to induce them to the proper conformations • Assist the formation of correct disulfide bonds How does chaperon work? docsity.com § 2.4 Quaternary Structure The quaternary structure is defined as the spatial arrangement of multiple subunits of a protein. docsity.com • Proteins need to have two or more polypeptide chains to function properly. • Each individual peptide is called subunit. • These subunits are associated through H-bonds, ionic interactions, and hydrophobic interactions. • Polypeptide chains can be in dimer, trimer .., as well as homo- or hetero- form. docsity.com lonic forces among Hb subunits NHS a igg2 S00 Be coo <3 — NH3* a we. C00" <a ae NH3* 8; Asp~ .. .His* terminal-COO- Asp~... Argt terminal-COO— wo Lys ... NH3+-terminal docsity.com  From primary to quaternary structure docsity.com • Constituents simple protein conjugated protein = protein + prosthetic groups Prosthetic group is non-protein part, binding to protein by covalent bond. This group can be carbohydrates, lipids, nucleic acids, phosphates, pigments, or metal ions. §2.5 Protein classification docsity.com