Chapter 2: Protein Composition and Structure PDF

CHAPTER 2. PROTEIN COMPOSITION AND STRUCTURE ◄ Crystals of human insulin  CHAPTER 2. PROTEIN COMPOSITION AND STRUCTURE  SEVERAL KEY PROPERTIES OF PROTEINS  Proteins are linear polymers built of monomer units called amino acids  Prot...

CHAPTER 2. PROTEIN COMPOSITION AND STRUCTURE ◄ Crystals of human insulin  CHAPTER 2. PROTEIN COMPOSITION AND STRUCTURE  SEVERAL KEY PROPERTIES OF PROTEINS  Proteins are linear polymers built of monomer units called amino acids  Proteins contain a wide range of functional groups Alcohols, thiols, thioethers, carboxylic acids, carboxamides and a variety of basic groups  Proteins can interact with one another and with other biological macromolecules to form complex assemblies  Some proteins are quite rigid, whereas others display a considerable flexibility  2.1 AMINO ACIDS  GENERAL PROPERTIES OF α-AMINO ACIDS  The building blocks of proteins  Most α-amino acids found in proteins are chiral Two isomers are in an enantiomeric form (D-form and L-form) Only L-amino acids are constituents of proteins Side chains Fig 2.4 The L and D isomers of amino acids.  2.1 AMINO ACIDS  GENERAL PROPERTIES OF α-AMINO ACIDS  Amino acids in solution at neutral pH exist predominantly as dipolar ions Fig 2.6 Ionization state as a function of pH.  2.1 AMINO ACIDS  TWENTY AMINO ACIDS  Twenty different amino acids are found in proteins  All proteins in all species from bacteria to human beings are constructed from the same set of 20 amino acids with a few exceptions  The remarkable range of protein functions results from the diversity and versatility of these 20 amino acids Hydrophobic, polar, positively charged, and negatively charged side chains  2.1 AMINO ACIDS  TWENTY AMINO ACIDS OH OH SH H2N CO2H H 2N CO 2H H2N CO2H H2N CO2H H2N CO2H Gly, G Ala, A Ser, S Thr, T Cys, C S N CO2H H H 2N CO 2H H2N CO2H H2N CO2H H2N CO2H Pro, P Val, V Leu, L Ile, I Met, M NH2 O OH O NH2 O O OH NH2 H2N CO 2H H2N CO2H H2N CO2H H2N CO2H H2N CO 2H Asp, D Asn, N Glu, E Gln, Q Lys, K HN NH2 NH N OH NH N H H2N CO2H H 2N CO 2H H2N CO 2H H2N CO2H H2N CO2H Arg, R His, H Phe, F Tyr, Y Trp, W  2.1 AMINO ACIDS  HYDROPHOBIC AMINO ACIDS  Glycine (Gly, G) Smallest, and achiral H2N CO2H  Alanine (Ala, A) A methyl group as its side chain  Valine (Val, V), Leucine (Leu, L), H 2N CO2H and isoleucine (Ile, I) Isoleucine has one more chiral center (S, S) H H2N CO2H H 2N CO2H H2N CO2H  2.1 AMINO ACIDS  HYDROPHOBIC AMINO ACIDS  Methionine (Met, M) S Met contains a largely aliphatic side chain that H2N CO2H includes a thioether group  Proline (Pro, P) N CO 2H The ring structure makes it more H conformationally restricted  Phenylalanine (Phe, F) and tryptophan (Trp, W) Contain aromatic side chains (phenyl and indole) NH H2N CO2H H 2N CO2H  2.1 AMINO ACIDS  POLAR AMINO ACIDS  Serine (Ser, S), threonine (Thr, T) and tyrosine (Tyr, Y) (2S, 3R) Contain hydroxyl groups; relatively reactive OH H OH Threonine contains additional chiral center H2N CO2H H2N CO2H OH  Asparagine (Asn, N) and glutamine (Gln, Q) Contain amide groups H 2N CO 2H  Cysteine (Cys, C) O O NH2 Contains a sulfhydryl group NH2 Reactive H2N CO 2H H2N CO 2H Forms disulfide bonds SH S S HN O HN H2N CO 2H O  2.1 AMINO ACIDS  POSITIVELY CHARGED AMINO ACIDS  Note pKa values of their side chains  Lysine (Lys, K) Has a primary amino group attached to a long alkyl chain  Arginine (Arg, R) NH 2 HN NH2 NH HN Has a guanidinium group N  Histidine (His, H) H2N CO2H H2N CO2H H 2N CO2H Contains an imidazole group (aromatic) Often found in the active sites of enzymes  2.1 AMINO ACIDS  NEGATIVELY CHARGED AMINO ACIDS  Note pKa values of their side chains  Aspartic acid (Asp, D) and glutamic acid (Glu, E) Contain a carboxylate At physiological pH, their side chains are negatively charged In some proteins, these side chains accept protons, and this ability is often functionally important O O OH OH H2N CO2H H2N CO2H  2.1 AMINO ACIDS  IONIZABLE AMINO ACIDS  2.1 AMINO ACIDS  ABBREVIATIONS FOR AMINO ACIDS  2.2 PRIMARY STRUCTURE OF PROTEINS  PEPTIDE BONDS  Proteins are linear polymers formed by linking the α-carboxyl group of one amino acid to the α-amino group of another amino acid – this linkage is called a peptide bond or an amide bond  The peptide bond formation is thermodynamically unfavorable However, peptide bonds are kinetically stable. Fig 2.13 Peptide bond formation.  2.2 PRIMARY STRUCTURE OF PROTEINS  POLYPEPTIDES  A series of amino acids joined by peptide bonds form a polypeptide chain.; each amino acid unit is called a residue.  By convention, the amino end is taken to be the beginning of a polypeptide chain Fig 2.14 Amino acid sequences have direction. YGGFL and LFGGY are different molecules.  2.2 PRIMARY STRUCTURE OF PROTEINS  THE POLYPEPTIDE BACKBONE  A polypeptide chain consists of a regularly repeating part, called the main chain or backbone and a variable part, the side chains  The polypeptide backbone is rich in hydrogen-bonding potential Can stabilize particular structures H-bond acceptor H-bond donor Fig 2.15 Components of a polypeptide chain.  2.2 PRIMARY STRUCTURE OF PROTEINS  PROTEINS  Most proteins contain 50–2000 amino acid residues The largest protein known is the muscle protein titin, which consists of more than 27,000 amino acids  The mean MW of an amino acid residue is about 110 g/mol  The linear polypeptide chain can be cross-linked The most common cross-links are disulfide bonds Fig 2.16 Cross-links. The formation of a disulfide bond from two cysteine residues is an oxidation reaction.  2.2 PRIMARY STRUCTURE OF PROTEINS  AMINO ACID SEQUENCES OF PROTEINS  Frederick Sanger In 1958 he was awarded a Nobel prize in chemistry "for his work on the structure of proteins, especially that of insulin" In 1980, Walter Gilbert and Sanger shared half of the chemistry prize "for their contributions concerning the determination of base sequences in nucleic acids"  2.2 PRIMARY STRUCTURE OF PROTEINS  AMINO ACID SEQUENCES OF PROTEINS  In 1953, Frederick Sanger determined the amino acid sequence of insulin A landmark in biochemistry The first protein sequence Showed that a protein has a precisely defined amino acid sequence consisting only of L amino acids linked by peptide bonds  Further studies in the late 1950s and early 1960s revealed that the amino acid sequences of proteins are determined by the nucleotide sequences of genes  2.2 PRIMARY STRUCTURE OF PROTEINS  PROTEIN SEQUENCING IS IMPORTANT  Essential to elucidating the catalytic mechanism of an enzyme Amino acid sequences are closely related to protein functions  Amino acid sequence is the link between the genetic message in DNA and the three-dimensional structure that performs a protein’s biological function  Sequence determination helps studying human diseases Alterations in amino acid sequence can produce abnormal function and disease (sickle-cell anemia and cystic fibrosis)  The sequence of a protein reveals much about its evolutionary history  2.2 PRIMARY STRUCTURE OF PROTEINS  PEPTIDE BONDS Fig 2.18 Peptide bonds are planar. Fig 2.20 Cis and trans peptide bonds. C─N 1.49 Å C=N 1.27 Å Fig 2.19 Typical bond lengths within a Fig 2.21 Cis and trans X-Pro bonds. These peptide unit. bonds have less preference for the trans bonds.  2.2 PRIMARY STRUCTURE OF PROTEINS  TORSION ANGLES  A measure of the rotation about a bond, usually taken to lie between -180 and +180 degrees (also called dihedral angles)  Two bonds between adjacent peptide bonds can rotate  This freedom of rotation about two bonds of each amino acid allows proteins to fold in many different ways. Fig 2.20 Rotation about bonds in a polypeptide.  2.2 PRIMARY STRUCTURE OF PROTEINS  TORSION ANGLES  Many combinations of φ and ψ are forbidden because of steric collisions between atoms Fig 2.23 A Ramachandran diagram. 2.3 SECONDARY STRUCTURE OF PROTEINS  Peptide chains can fold into regular structures such as the alpha helix, the beta sheet, and turns and loops  Secondary structure of proteins is the general three-dimensional form of local segments of proteins  In proteins, the secondary structure is defined by the patterns of hydrogen bonds between backbone amide and carboxyl groups  The secondary structure may be also defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot  2.3 SECONDARY STRUCTURE OF PROTEINS  THE ALPHA HELIX  A common motif in the secondary structure of proteins  A right-handed coiled or spiral conformation  Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier Fig 2.24 Structure of the α helix.  2.3 SECONDARY STRUCTURE OF PROTEINS  THE ALPHA HELIX  Except for amino acids near the ends of an  helix, all the main chain CO and NH groups are hydrogen bonded  Structure of the  helix 3.6 residues per turn 0.15 nm translation per residue 0.54 nm per turn Fig 2.25 Hydrogen-bonding scheme for an  helix.  2.3 SECONDARY STRUCTURE OF PROTEINS  THE ALPHA HELIX  The Ramachandran diagram reveals that both the right- handed and the left-handed helices are among allowed conformations  Right-handed helices Energetically more favorable Less steric clash between the side chains and the backbone All  helices found in proteins are right-handed Fig 2.26 Ramachandran diagram for helices.  2.3 SECONDARY STRUCTURE OF PROTEINS  THE ALPHA HELIX  Amino acid preference in the  helix Branching at the -carbon atom destabilizes  helices; Val, Thr, and Ile H-bond donors or acceptors in close proximity to the main chain disrupt  helices; Ser, Asp, and Asn Pro also is a helix breaker; no NH group; ring structure  The -helical content of proteins ranges widely, from none to almost 100%  2.3 SECONDARY STRUCTURE OF PROTEINS  THE ALPHA HELIX  About 75% of the residues in ferritin are in  helices  About 25% of all soluble proteins are composed of  helices connected by loops and turns of the polypeptide chain Fig 2.27 Schematic views of  helices. Fig 2.28 A largely -helical protein, ferritin.  2.3 SECONDARY STRUCTURE OF PROTEINS  BETA SHEETS  A helical arrangement with an extremely elongated form  Two residues per turn; 0.34 nm transition distance per residue; 0.7 nm transition distance per turn  Stabilized by inter-strand H-bonding Fig 2.30 Structure of a β strand. Fig 2.29 Ramachandran diagram for β strands.  2.3 SECONDARY STRUCTURE OF PROTEINS  BETA SHEETS Fig 2.31 and 2.32 Parallel and antiparallel β sheets  2.3 SECONDARY STRUCTURE OF PROTEINS  BETA SHEETS Fig 2.35 A protein rich in β sheets. The structure of a fatty acid-binding protein. Fig 2.33 Structure of a mixed β sheet. Fig 2.34 A schematic twisted β sheet.  2.3 SECONDARY STRUCTURE OF PROTEINS  TURNS AND LOOPS  Have a universal role of enabling the polypeptide to change direction  In many reverse turns, the CO group of residue i of a polypeptide Fig 2.36 Structure of a reverse turn. is hydrogen bonded to the NH group of residue i+3.  Turns and loops invariably lie on the surfaces of proteins and thus often participate in interactions between proteins and other molecules Fig 2.37 Loops on an antibody surface.  2.3 SECONDARY STRUCTURE OF PROTEINS  FIBROUS PROTEINS – α-keratin and collagen  α-keratin The primary component of wool, hair, and skin Two right-handed α-helices form a type of left-handed superhelix; α-helical coiled coil A member of a superfamily of coiled-coil proteins Fig 2.38 An α-helical coiled coil.  2.3 SECONDARY STRUCTURE OF PROTEINS  FIBROUS PROTEINS – α-keratin and collagen  α-keratin Cross-linked by van der Waals and ionic interactions 3.5 residues (not 3.6) per turn in the left-handed supercoli; haptad repeats Interstrand disulfide bonds Interstrand interactions determine the physical properties of coiled-coil proteins Fig 2.39 heptad repeats in a coiled-coil protein.  2.3 SECONDARY STRUCTURE OF PROTEINS  FIBROUS PROTEINS – α-keratin and collagen  Collagen The most abundant protein of mammals The main fibrous component of skin, bone, tendon, cartilage, and teeth Rod-shaped; 300 nm long and 1.5 nm in diameter Contains three helical polypeptide chains (~ 1000 AA residues) Gly-Pro-Hyp repeats Fig 2.40 Amino acid sequence of a part of a collagen chain.  2.3 SECONDARY STRUCTURE OF PROTEINS  FIBROUS PROTEINS – α-keratin and collagen  Collagen Fig 2.42 Structure of the protein collagen. No hydrogen bond within a strand The helix is stabilized by steric repulsion of the pyrrolidine rings Interstrand hydrogen bonds (NH of The only residue that can fit in an Gly and CO on the other chains); the interior position is glycine OH group of Hyp also participates in hydrogen bonding Fig 2.41 Conformation of a single strand of a collagen triple helix.  2.3 SECONDARY STRUCTURE OF PROTEINS  FIBROUS PROTEINS – α-keratin and collagen  Collagen-related diseases Osteogenesis imperfecta ( ), brittle bone disease, blue sclera; caused by Scurvy ( ); cause by replacement of Gly with a vitamin C deficiency (vitamin C bulky amino acid is essential for the collagen synthesis)  2.4 TERTIARY STRUCTURE OF PROTEINS  TERTIARY STRUCTURE  Secondary structure is the general three-dimensional form of local segments of proteins  Tertiary structure is the overall three-dimensional structure of proteins  X-ray crystallography and NMR spectroscopy  Protein Data Bank (PDB) has over 80,000 structures X-ray crystal structure of http://www.pdb.org myoglobin  Number 0 10000 20000 30000 40000 50000 60000 70000 80000 90000 Year 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997  TERTIARY STRUCTURE 1996 1995 1994 1993 1992 1991 1990 Year 1989 1988 1987  Data produced by the Protein Data Bank 1986 1985 1984 1983 1982 1981 1980 1979 1978 1977 1976 1975 1974 1973 1972 2.4 TERTIARY STRUCTURE OF PROTEINS  2.4 TERTIARY STRUCTURE OF PROTEINS  MYOGLOBIN  Myoglobin is an iron- and oxygen-binding (carrier) protein found in the muscle tissue of vertebrates in general and in almost all mammals  A single-chain globular protein of 153 AAs, containing a heme (iron-containing porphyrin) prosthetic group  Myoglobin occupies a pivotal position in the history of protein science; the first protein structure (1958) by John Kendrew  Many of the structure-function relationships discovered for myoglobin have proved to be of considerable importance to the activity of other proteins  An extremely compact molecule (4.5 X 3.5 X 2.5 nm); 70% α helices, and 30% turns and loops  2.4 TERTIARY STRUCTURE OF PROTEINS  Interactions stabilizing tertiary structure  Disulfide bridges Dictate a protein fold by forming strong covalent links between Cys side chains Disulfide bonds are only broken at high temperatures, acidic pH or in the presence of reductants In BPTI reduction of the disulfide bonds leads to decreased protein stability Bovine pancreatic trypsin inhibitor (BPTI)  2.4 TERTIARY STRUCTURE OF PROTEINS  Interactions stabilizing tertiary structure  The hydrophobic effect The observed tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules Structures of water-soluble proteins have a hydrophobic core in which side chains are buried from water, which stabilizes the folded state. Minimizing the number of hydrophobic side chains exposed to water is the principal driving force behind the folding process An entropic effect originating from the disruption of highly dynamic hydrogen bonds between molecules of liquid water by the nonpolar solute.  2.4 TERTIARY STRUCTURE OF PROTEINS  Interactions stabilizing tertiary structure  Charge-charge interactions Mainly by Lys, Arg, His / Asp, Glu; to a lesser extent Tyr and Cys Interactions with water or solvent molecules dramatically weaken the charge-charge interaction The interaction can be significantly greater within nonpolar regions in proteins An example of charge- charge interactions occurring in proteins (chymotrypsin)  2.4 TERTIARY STRUCTURE OF PROTEINS  Interactions stabilizing tertiary structure Fig 2.44 Distribution of amino acids in myoglobin. Hydrophobic amino acids shown in yellow, charged amino acids in blue, and others in white. (B) is a cross-sectional view of (A)  2.4 TERTIARY STRUCTURE OF PROTEINS  Interactions stabilizing tertiary structure  Hydrogen bonding Contributes significantly to the overall stability of the tertiary structure or folded state (stabilizing α helices and β strands) Involves a donor and acceptor atom Varies in length from 0.26 to 0.34 nm  2.4 TERTIARY STRUCTURE OF PROTEINS  Interactions stabilizing tertiary structure  Van der Waals interactions Occur between adjacent, uncharged and non-bonded atoms; 1) permanent dipoles, 2) permanent and temporary dipoles, and 3) temporary, induced dipoles Important in protein folding Van der Waals interaction as a function of interatomic distance r.  2.4 TERTIARY STRUCTURE OF PROTEINS  PORINS  β-barrel proteins that cross a cellular membrane and act as a pore through which molecules can diffuse  These proteins are covered on the outside largely with hydrophobic residues; the center of the protein contains many charged and polar amino acids  “Inside out” structure Fig 2.45 “Inside out” amino acid distribution in porin.  2.4 TERTIARY STRUCTURE OF PROTEINS  MOTIFS AND DOMAINS  A compact three-dimensional protein structure of several adjacent elements of secondary structure; combinations of secondary structure; supersecondary structure  Protein domains – a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain Fig 2.46 The helix-turn-helix motif, a supersecondary structural element. Fig 2.47 Protein domains. The cell-surface protein CD4 consists of four similar domains.  2.5 QUATERNARY STRUCTURE OF PROTEINS  QUATERNARY STRUCTURE  The arrangement of multiple folded proteins in a multi-subunit complex  Each polypeptide chain in this complex is called a subunit Fig 2.48, 49 and 50 the Cro protein of bacteriophage λ, the α2β2 tetramer of human hemoglobin, and the complex quaternary structure of human rhinovirus.  2.6 SEQUENCE AND STRUCTURE  SEQUENCE SPECIFIES CONFORMATION  Protein denaturation and refolding experiments Fig 2.52 Role of β-mercaptoethanol in reducing Fig 2.51 Amino acid sequence of disulfide bonds. bovine ribonuclease. Fig 2.53 Reduction and denaturation of ribonuclease.  2.6 SEQUENCE AND STRUCTURE  SEQUENCE SPECIFIES CONFORMATION  Denatured proteins do not have catalytic activity, but refolding regained the activity.  Denatured proteins can be refolded by dialysis in the absence of urea and β-mercaptoethanol  Some proteins are not refolded efficiently due to misfolding or aggregation  Chaperones facilitate folding processes Fig 2.54 Reestablishing correct disulfide pairing.  2.6 SEQUENCE AND STRUCTURE  SECONDARY STRUCTURES AND AMINO ACIDS  Ala, Glu, and Leu tend to be present in α-helices  Val, Thr, and Ile tend to destabilize α-helices because of steric clashes; these residues are readily accommodated in β-strands  Ser, Asp, and Asn tend to disrupt α-helices because they can form H-bonds with the backbone  Pro tends to disrupt both α-helices and β-strands because of lack of the NH group and its ring structure  Accurate predictions of secondary structure are difficult because the context (environment) is often crucial Fig 2.55 Alternative conformations of a peptide sequence. Many sequences can adopt alternative conformations in different proteins.  2.6 SEQUENCE AND STRUCTURE  SECONDARY STRUCTURES AND AMINO ACIDS  2.6 SEQUENCE AND STRUCTURE  PROTEIN FOLDING IS A COOPERATIVE PROCESS  A sharp transition from the native form to the denatured form (“all or none” process)  This process results from a cooperative transition; unfolding some part of a protein will destabilize the remainder of the structure Fig 2.57 Transition from folded to unfolded state and components of a partly denatured protein solution. In a half-unfolded protein solution, half the molecules are fully folded and half are fully unfolded. However, transient and unstable intermediate structures may exist.  2.6 SEQUENCE AND STRUCTURE  LEVINTHAL’S PARADOX  Enormous difference between calculated and actual folding times  Folding time for a small protein with 100 AA by a random search Each residue can assume three different conformations It takes 10-13 s to convert one structure into another 3100 X 10-13 s = 1.6 X 1027 years  This means that proteins do not fold by trying every possible conformation  2.6 SEQUENCE AND STRUCTURE  TYPING-MONKEY ANALOGY  Richard Dawkins “ The Blind Watchmaker”  Cumulative Selection N29 when you know the length of the sentence (N, the number of letters on a keyboard) If each correct character is retained, a few thousand keystrokes would be enough to type the sentence  2.6 SEQUENCE AND STRUCTURE  THE NUCLEATION-CONDENSATION MODEL  The essence of protein folding is the tendency to retain partly correct intermediates Fig 2.59 Proposed folding pathway of chymotrypsin inhibitor. Local regions with sufficient structural preference tend to adopt their favored structures initially (1) These structures come together to form a nucleus with a nativelike, but still mobile, structure (4) This structure then fully condenses to form the native, more rigid structure (5)  2.6 SEQUENCE AND STRUCTURE  FOLDING FUNNEL  The energy surface for the overall process of protein folding can be visualized as a funnel  The wide rim represents the wide range of structures accessible to the ensemble of denatured protein molecules  As the free E of the population decreases, fewer conformations are accessible  At the bottom of the funnel is the folded state with its well-defined conformation  Many paths can lead to this same E minimum Fig 2.60 Folding funnel.  2.6 SEQUENCE AND STRUCTURE  PREDICTION OF 3D STRUCTURE OF PROTEINS  The prediction of 3D structure from sequence has proved to be extremely difficult  The local sequence determine only 60-70% of the secondary structure  Long-range interactions are required to fix the full secondary structure and the tertiary structure  2.6 SEQUENCE AND STRUCTURE  PREDICTION OF 3D STRUCTURE OF PROTEINS  ab initio prediction Predicts the folding of an AA sequence without prior knowledge Computer-based calculations are employed to minimize the free E of a structure Limited by the vast number of possible conformations, the marginal stability of proteins, and the subtle energetics of weak interactions in aqueous solution  Knowledge-based prediction An AA sequence of unknown structure examined for compatibility with known protein structures or fragments If a significant match is detected, the known structure can be used as an initial model  2.6 SEQUENCE AND STRUCTURE  MULTIPLE STRUCTURES  Some proteins can adopt two different structures  Intrinsically unstructured proteins (IUP) They, completely or in part, do not have a stable tertiary structure under physiological conditions Unstructured regions are rich in charged or polar AAs They assume a defined structure on interaction with other proteins  Metamorphic proteins They exist in an ensemble of structures of approximately equal energy that are in equilibrium  2.6 SEQUENCE AND STRUCTURE  MULTIPLE STRUCTURES  Metamorphic proteins They often have different binding partners and therefore different functions  These example shows protein diversity encoded from a single gene Fig 2.61 Lymphotactin exists in two conformations, which are in equilibrium.  2.6 SEQUENCE AND STRUCTURE  PROTEIN MISFOLDING AND DISEASES  Many diseases are associated with improperly folded proteins Alzheimer disease, Parkinson disease, Huntington disease, and transmissible spongiform encephalopathies (prion disease) These diseases result in the deposition of protein aggregates, called amyloid fibrils or plaques In these diseases, soluble proteins are converted into insoluble fibrils rich in β sheets  Transmissible spongiform encephalopathy Infectious neurological diseases transmitted by agents consisted only of proteins Bovine spongiform encephalopathy (mad cow disease), Creutzfeld-Jacob disease (human), scrapie (sheep), and chronic wasting disease (deer and elk)  2.6 SEQUENCE AND STRUCTURE  PROTEIN MISFOLDING AND DISEASES  Prions An infectious agent composed of a protein, called PrP Responsible for the transmissible spongiform encephalopathies in a variety of mammals They act as a template to guide the misfolding of more proteins into prion form Fig 2.62 A model of the human prion Fig 2.63 The protein-only model for prion- protein amyloid. disease transmission.  2.6 SEQUENCE AND STRUCTURE  PROTEIN MODIFICATION  Proteins are able to perform numerous functions that rely solely on the versatility of their 20 building blocks  Many proteins are covalently modified through the attachment of groups other than amino acids These modifications expand their functions  Acetylation N-terminal; resistance to degradation  Hydroxylation Proline; stabilizing fibers of newly synthesized collagen  Glycosylation  Phosphorylation Reversible switches in regulating cellular processes  2.6 SEQUENCE AND STRUCTURE  PROTEIN MODIFICATION  Chemical rearrangements of side chains and the peptide backbone Green fluorescent protein (GFP)  Cleavage Activation of inactive precursors Fig 2.65 Chemical rearrangement in GFP.