Biochem Sheet 17 PDF

17 Ibrahim Aldarbi Aya Alnatour Nabil Bashir β pleated sheet (β sheet) • Another element of the secondary structure. • They are composed of two or more straight chains (β strands) that are hydrogen bonded side by side (it’s the force that stabilize this element). β strand • It’s zig-zag like stru...

17 Ibrahim Aldarbi Aya Alnatour Nabil Bashir β pleated sheet (β sheet) • Another element of the secondary structure. • They are composed of two or more straight chains (β strands) that are hydrogen bonded side by side (it’s the force that stabilize this element). β strand • It’s zig-zag like structure, with very small coil (not comparable to the coil of alpha helix). • Optimal hydrogen bonding occurs when the sheet is bent (pleated) to form β-pleated sheets, these inter hydrogen bonds (in alpha helix they are intra not inter) are between the hydrogen atom in the amino group and the oxygen in the carbonyl group. More on β-sheets • β sheets can form between many strands, typically 4 or 5 but as many as 10 or more. • Such β sheets can be purely antiparallel (the N-terminus of the first strand is facing the C-terminus of the second strand), purely parallel (the Nterminus of the first strand is facing the N-terminus of the second strand), or mixed. Parallel Antiparallel More on β-sheets Antiparallel The arrows represent the beta sheet, if they are pointing at the same direction, then the beta sheet is parallel, if they are pointing at opposite direction, then the beta sheet is antiparallel. Modified • This is a supra-secondary structure, how we can identify it? • When we see two (or more) elements (same type or different types) connected (by beta turns) to each other. Effect of amino acids • Usually, hydrophobic amino acids tend to form beta sheet. • If you see a series of hydrophobic amino acids, and at one terminal positively charged amino acid and at the other terminal negatively charged amino acid, that indicates a present of alpha helix. • Valine, threonine and Isoleucine with branched R groups at β-carbon and the large aromatic amino acids (phenylalanine, tryptophan, and tyrosine) tend to be present in β-sheets. • Proline tends to disrupt β strands • Remember that the proline is a broker, it won’t form hydrogen bonds. How are they illustrated/drawn? You need to know how each element is presented in the molecular structure. Molecular structure Molecular structure β-turns • Turns are compact, U-shaped secondary structures • They are also known as β turn or hairpin bend • Permits the change of direction of the peptide chain to get a folded stricture • Carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away. • They consist of four amino acids, two of them are glycine (must be the second or the third, to make the turn small) and proline (must be the second or the third, because the first and the fourth must be hydrogen bonded, any polar amino acids will do the job). • As said before, turns connect other elements together. Loops and coils • Loops (bigger than turns) are a diverse class of secondary structures in proteins with irregular geometry and that connect the main secondary structures. • They are found on surface of molecule (and contain polar residues) and provide flexibility to proteins. • Amino acids in loops are often not conserved (random, another difference to turns). • Hairpin loops-often anti-parallel beta strands • Help the protein to fold. Super-Secondary Structures • They are regions in proteins that contain an ordered organization of secondary structures. • More than one secondary structure element connected to each other • There are at least types: • Motifs: short conserved sequence pattern supersecondary structures, • Domains : distinct structural and functional unit that is larger than a motif. • Motifs may be found within domains and multiple motifs can make a domain • In conclusion, two or more super-secondary structures = motif, two or more motifs = domain. A motif (a module) • A motif is a repetitive supersecondary structure, which can often be repeated and organized into larger motifs. • It usually constitutes a small portion of a protein (typically less than 20 amino acids). • In general, motifs may provide us with information about the folding of proteins, but not the biological function of the protein. • Motifs are important in some proteins; they help in binding specific ligands to that protein. Examples of motifs Helix-loop-helix is found in many proteins that bind DNA. It is characterized by two α-helices connected by a loop. Helix-turn-helix is a structural motif capable of binding DNA. It is composed of two α helices joined by a short strand of amino acids Modified Specific element (alpha helix or beta sheet) Folding motifs on each other Stages of protein folding Super-secondary structure (two elements or more connected by turns or loops). Folding domains on each other Some proteins will aggregate more than one subunit Proteins that form quaternary structure, will be functional at this structure, not at the tertiary structure. Tertiary structure TERTIARY STRUCTURE? • The overall conformation of a polypeptide chain, how every atom in the chain is found in the three-dimensions. • The three-dimensional arrangement of all the amino acids residues • The spatial arrangement of amino acid residues that are far apart in the sequence How to look at proteins… The ways that the tertiary structure are presented in the books Protein surface map Space filling structure Trace structure Ribbon structure Cylinder structure Ball and stick structure Shape-determining forces (stabilizing forces) In the secondary structure, the interactions are short-range, meanwhile in the tertiary structure they are long-range, the amino acid number 5 may interact with the amino acid number 500, because the folding make them close to each other. Shape-determining forces (stabilizing forces) Intra-hydrogen bonds in the alpha helices. Inter-hydrogen bonds in the beta sheets. Shape-determining forces (stabilizing forces) Between R groups, remember that R groups have nothing to do in the secondary structure, but in the tertiary they are important. Shape-determining forces (stabilizing forces) Electrostatic (ionic) interaction This is the epsilon amino lysine, where the alpha is busy in the formation of the peptide bond, it may form hydrogen bond. It’s positively charged because its pKa is higher than the physiological pH, it will be protonated. pKa=10 Shape-determining forces (stabilizing forces) Electrostatic (ionic) interaction This is the aspartic acid, it’s negatively charged because its pKa is lower than the physiological pH, it will be deprotonated. pKa=3.544 Shape-determining forces (stabilizing forces) Gln (glutamine) Not charged and polar, so it can from hydrogen bond Ser (serine) Shape-determining forces (stabilizing forces) All previous mentioned bonds are non-covalent, meanwhile what we are going to talk about now is covalent: disulfide bond. It’s formed between two cysteines, forming a structure called cystine. Non-covalent interactions • Hydrogen bonds occur not only within and between polypeptide chains but with the surrounding aqueous medium. • Charge-charge interactions (salt bridges) occur between oppositely Again, Asp and Lys. charged R-groups of amino acids. • Charge-dipole interactions form between charged R groups with the partial charges of water. The same charged group can form either hydrogen bonding or electrostatic interactions van der Waals attractions • Doctor skipped this slide and said it isn’t important. • There are both attractive and repulsive van der Waals forces that control protein folding. • Although van der Waals forces are extremely weak, they are significant because there are so many of them in large protein molecules. Hydrophobic interactions • A system is more thermodynamically (energetically) stable when hydrophobic groups are clustered together rather than extended into the aqueous surroundings. • Always, when the protein folds, all hydrophobic amino acids will escape far away from water, and they will be associated with each other inside the protein forming hydrophobic interaction, meanwhile hydrophilic amino acids will be on the surface of the protein forming hydrogen bonds with the water. POSSIBLE SEQUENCE OF EVENTS IN FOLDING R HYDROPHOBIC COLLAPSE ↓ T As said before, hydrophobic amino acids will escape far away from the water. E NUCLEATION(short range, ordered sec st) ↓ E A SUPERSECONDARY STRUCTURE ↓ R R STRUCTURAL DOMAINS ↓ T Found by folding two or more supersecondary structures. R FUNCTIONAL DOMAINS ↓ I It’s the cleft between two structural domains. A QUATERNARY (IF) ↓ A N PROSTHETIC GROUPS, PROCESSING(IF) ↓ R E ______ ACTIVITY Y -ΔG= (-9 TO -15) -ΔG=ΔH-ΔS Added if the protein needs them. All these process is controlled by it and must be negative, ΔS highly positive. Can polar amino acids be found in the interior?...YES • Polar amino acids can be found in the interior of proteins • In this case, they form hydrogen bonds to other amino acids or to the polypeptide backbone • They play important roles in the function of the protein • As an example, the integral proteins that span the membrane, and in the spanning region we can find hydrophilic amino acids, why? • To allow the passage of ions or polar molecules through the membrane. Disulfide bonds • The side chain of cysteine contains a reactive sulfhydryl group (—SH), which can oxidize to form a disulfide bond (—S—S—) to a second cysteine. • The crosslinking of two cysteines to form a new amino acid, called cystine. • This is done by atmospheric oxygen. Metal ions • Several proteins can be complexed to a single metal ion that can stabilize protein structure by forming: • Covalent interaction (myoglobin-iron) (hemoglobin-iron) • Salt bridges (carbonic anhydrase-zinc) • This metals are important in binding or catalysis too. Myoglobin Carbonic anhydrase Domains and folds • A domain is a combination of α helices and/or β sheets that are connected to each other via turns, loops, and coils and are organized in a specific three-dimensional structure. • A domain may consist of 100–200 residues. • Domains fold independently of the rest of the protein or of other domains within the same protein. • Similar domains can be found in proteins with similar function and/or structure and can be present in different proteins (but in this case the protein must have another domain that is specific to its function, such as dehydrogenases enzymes). • Domains may also be defined in functional terms • enzymatic activity • binding ability (e.g., a DNA-binding domain) • When a domain or multiple domains within a protein possess specific functions, they are known as Folds. • The actin fold • The nucleotide binding fold α-helices as transmembrane domains • Membrane-spanning proteins contain a transmembrane domain that is an α–helix made of hydrophobic amino acids (at the surface of the protein, inside the protein we find hydrophilic amino acids). • Some membrane proteins contain several transmembrane domains that are also αhelices. • For receptors, the helices are connected by loops containing hydrophilic amino acid side chains that extend into outside of both sides of the membrane. • Membrane ion channels contain amphipathic α–helices.