4 1 MCB 450 Lecture 4 Tertiary and Quaternary Structure of Proteins Globular Proteins Motifs and Domains Fibrous Proteins Collagen Protein Bioinformatics Protein Folding Denaturation Post translational Modifications of Proteins Amyloidoses 4 2 Tertiary structure 3 D folding of a polypeptide i simple combinations of 2 structural elements motifs or folds ii combination of motifs folds into domains 4 3 Globular fibrous membrane proteins Globular soluble and compact many are cytoplasmic some secreted from cells Fibrous insoluble long strands or sheets repeating unit of 2 structure many similar polypeptides tightly packed Membrane embedded in membranes many have 1 helical stretches that span a membrane 4 4 3 D Structure of globular proteins Conformation spatial arrangement of atoms in a protein Units of 2 structure connecting loops are folded into spherical or globular shapes Units often made up of several types of 2 structure Many different 3 D structures many different functions e g enzymes regulatory proteins DNA binding Conformational changes possible usually depend on binding of a ligand Hierarchical classification of protein structure motifs or folds make up domains 4 5 Common structural motifs folds in globular proteins Motif fold stable arrangement of 2 or more elements of 2 structure the connection s between them helix loop helix or helix turn helix e g in DNA binding proteins EF hand motif in Ca2 binding proteins 4 6 Common structural motifs folds in globular proteins Active site those involved in catalysis often in this loop hairpin motif antiparallel strands motif parallel strands separated by helix 4 7 Many arrangements of strands are possible of strands their relative orientation and how the strands are connected along the polypeptide chain strand order vary e g Color coding here is just intended to help identify each strand in 3D structure No knots 4 8 Extended sheets can roll up to form barrels 4 9 Domains Several motifs form a protein domain Domain fundamental unit of tertiary structure One polypeptide chain can have several domains Domains can have different functions 4 10 Constructing domains from motifs barrel consists of a series of loops arranged so that the strands form a barrel motif fold domain made up of motifs 4 11 Two proteins built from motifs barrels in triosephosphate isomerase 8 parallel strands Open twisted sheet found in some dehydrogenases 4 12 Loops often contain responsible for catalytic activity e g in an enzyme with an barrel structure the strands and helices form the structural framework of the enzyme and the active site is formed by loops at one end of the barrel e g ribulose bisphosphate carboxylase C5 CO2 2 C3 in CO2 fixation Charged side chains in blue substrate red 4 13 Domains may have distinct functions even when separated Troponin C each domain can individually bind calcium NXF1 protein involved in RNA export from nucleus C Nuclear transport factor like domain RNA binding Leucine rich repeats N p15 binding domain 4 14 What about the side chains 3 structure of myoglobin 8 helical segments 70 of myoglobin s Space filling model with all amino acid side chains heme Side chains of hydrophobic in blue most are in the interior of the myoglobin molecule giving a dense hydrophobic core from which most H2O is excluded 4 15 Protein conformation doesn t always stay the same conformational changes possible especially when a ligand binds Ras protein Flips between an active an inactive conformation GDP GTP Mutated to active conformation in 25 of human cancers OFF Lymphotactin An extreme case i Chemokine form 3 strand sheet C terminal helix ii Carbohydrate binding dimer of all sheets http www laas fr N2IS EN 28 32225 Structural oncology php ON SIGNALS GROWTH 4 16 Quaternary structure Many proteins have multiple polypeptide subunits Multisubunit proteins may contain two or more identical polypeptides or may include different polypeptides 4 structure usually stabilized by weak non covalent interactions between exposed on the surfaces of the polypeptide subunits same forces that stabilize the tertiary structures of proteins The 2 2 tetramer of human hemoglobin 4 17 Fibrous proteins Polypeptide chains organized in long strands or sheets Fundamental structural unit is a simple repeating unit of 2 structure many similar polypeptide chains are packed tightly together to form elaborate supramolecular complexes Hydrophobic and insoluble e g keratin silk 4 18 keratin a fibrous protein 2 helices oriented in parallel left handed super twisted Surfaces where helices touch made up of hydrophobic with R groups meshed together in regular interlocking pattern Structure further stabilized by S S cross links between keratin polypeptides Rich in Ala Val Leu Ile Met Phe 4 19 4 20 Protein 3D structure silk fibroin a fibrous protein Layers of antiparallel sheets rich in Ala Gly permit close packing of sheets with interlocking arrangement of R groups stabilized by H bonding between all peptide linkages in each strand http www nanowerk com spotlight spotid 4523 php 4 21 Collagen a unique triple helical structure Repeating Gly X Y tripeptide in each strand forms a helix w 3 per turn X Pro Y hydroxyPro Hyp Hyp at the right place is critical for collagen stability NO H bonds in an individual collagen strand each stand stabilized by steric repulsion between the pyrrolidine rings of Pro and Hyp 4 22 Collagen a unique triple helical structure Three collagen helices are twisted around each other to form a superhelical cable The triple helical cable is stabilized by H bonds between peptide NH groups of Gly and C O groups on on adjacent chains 4 23 Hydroxyproline is made from Pro by an enzyme ENZYMATIC CONVERSION DEPENDS ON ASCORBATE VITAMIN C Collagen main fibrous component in skin tendon cartilage bone Vitamin C deficiency leads to less Hyp collagen instability and scurvy 4 24 Titin mouse Proteins can be large and small 3 906 487 35 213 The mean mol wt mass of an is 110 Da 4 25 How we detect 1 sequence relationships sequence alignments Compare 1 sequences of 2 proteins Align sequences to maximize identical and similar positions similar similar in side chain properties D E R K L I V etc The more closely related two sequences are the higher the identity and similarity along the sequence Allows identification of Proteins w same function from different organisms Proteins w same or different but related functions from same or different organism Can also use a new sequence to search