Protein Structure PDF

Protein structure BIOCHEMISTRY-DENTAL, IST SEMESTER, 2023 Four Levels of Protein structure Primary structure of a protein is the sequence of amino acid residues that constitute the polypeptide chain and the sequence positions of disulfide bonds Secondary structure description of its peptide backbo...

Protein structure BIOCHEMISTRY-DENTAL, IST SEMESTER, 2023 Four Levels of Protein structure Primary structure of a protein is the sequence of amino acid residues that constitute the polypeptide chain and the sequence positions of disulfide bonds Secondary structure description of its peptide backbone conformations, i.e., which of its peptide bonds are in α-helix, β-sheet, β-turn, or unordered conformations. The secondary structure of a typical peptide chain in globular proteins VARIES continuously throughout the length of the chain. the secondary structure of chains in fibrous proteins are usually constant throughout the length of chains. The pattern of how the individual stretches of α-helix and β-sheet are arranged relative to one another in three dimentional space is called SUPERSECONDARY STRUCTURE. Tertiary structure refers to the three-dimensional structure(conformation) of a polypeptide chain, that is, the three-dimensional arrangement of all atoms in each amino acids residues. VERY COMPACT, irregular-spheres. STRUCTURAL DOMAINS & FUNCTIONAL DOMAINS Some proteins are made of multiple polypeptides connected with each other. These are known as multimeric proteins. Quaternary structure describes the number and relative positions of the subunits in a multimeric protein. A condensation reaction: PEPTIDE BOND FORMATION Proteins are linear polymers formed by covalently linking the α-carboxyl group of one amino acid to the α-amino group of another amino acid with a peptide bond (also called an amide bond). The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule in a condensation reaction that is energetically unfavorable. Definitions Each amino acid unit in a polypeptide is called a residue. The short chain of amino acids is known as an oligopeptides - fewer than 20-30 amino acid residues Longer peptides are referred to as polypeptides- contain as many as 1000 residues. Directionality of reading A polypeptide chain has polarity because its ends are different, with an αamino group at one end and an α-carboxyl group at the other. The amino end is the beginning of a polypeptide chain. Backbone and side chains A polypeptide chain consists of a regularly repeating part, called the main chain or backbone, and a variable part, comprising the distinctive side chains. PEPTIDE BOND PLANES Peptide bonds have double bond character, electrons are delocalized over the O-C-N One consequence is six atoms end up confined to a peptide plane as shown. Side chains freely rotate Adjacent peptide planes along a peptide chain can rotate with respect to each other at the α– carbon atom. Only certain angles are possible between adjacent planes; steric hindrance, group bumping into each other prevent all other angles. The groups of each peptide bond plane must move together, they cannot move independently. Only certain angles are allowed between adjacent peptide bond planes due to steric himdrance. It has a zig-zag structure and is planar. It has a double bond character rigid. Importance of the Primary Structure Primary structure of a protein is the sequence of amino acid residues that constitute the polypeptide chain and the sequence positions of disulfide bonds • Example: Leu—Gly—Thr—Val—Arg—Asp—His The primary structure of a protein determines the other levels of structure. A single amino acid substitution can give rise to a malfunctioning protein, as is the case with sickle-cell anemia. Sickle cell hemoglobin (HbS) • Hemoglobin: 2 α-chains (2x 141aa)+2 βchains(2x146)=574aa • On each β-chain at position 6: val instead of glu 2/574 . • It is caused by a change of amino acids in the 6th position of β globin (Glu to Val).-type change • pI: 6.87→7.09 • The mutation results in: arrays of aggregates of deoxy hemoglobin molecules,→insoluble FIBERS intracellularly → cell fragile (anemia) deformation of the red blood cell, → clogging in blood vessels and tissues→ischemia→anoxia→cell necrosis→extreme pain. • Trait: rarely symptomatic • Trait selective advantage against consequences of malaria • Patients have variable frequency and severity of crisis SECONDARY STRUCTURE • The two bonds within each amino acid residue freely rotate. • the bond between the α-carbon and the amino nitrogen • the bond between the α-carbon and the carboxyl carbon • • A hydrogen-bonded, local arrangement of the backbone of a polypeptide chain. Polypeptide chains can fold into regular structures such as: • Alpha helix • Beta-pleated sheet • Turns • Loops The α helix • The peptide chain could be twisted or coiled clockwise (right handed) or counterclockwise(left handed) • Peptides with L-amino acids form right handed • The helix has an average of 3.6 amino acids per turn. • The pitch of the helix (the linear distance between corresponding points on successive turns) is 3.6 X 0.15=0.54 nm • It is very stable because of the linear hydrogen bonding. • The trans side chains of the amino acids project outward from the helix, thereby avoiding steric hindrance with the polypeptide backbone and with each other. Amino acids NOT found in α-helix • Glycine: too small-strong broker • Proline- strong broker • No rotation around N-Cα bond • No hydrogen bonding of α-amino group • Close proximity of a pair of charged amino acids with similar charges • Amino acids with branches at the β-carbon atom (valine, threonine, and isoleucine) β pleated sheet (β sheet) • They are composed of two or more straight chains (β strands) that are hydrogen bonded side by side. β strand • Optimal hydrogen bonding occurs when the sheet is bent (pleated) to form βpleated sheets. 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, purely parallel, or mixed. Parallel Antiparallel Effect of amino acids • 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 How are they illustrated/drawn? 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. • Glycine and proline are commonly present in turns • Why? Loops and coils • Loops 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. • Hairpin loops-often anti-parallel beta strands Super-Secondary Structures • They are regions in proteins that contain an ordered organization of secondary structures. • 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 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. 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 Tertiary structure TERTIARY STRUCTURE? • The overall conformation of a polypeptide chain • 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… Protein surface map Space filling structure Trace structure Ribbon structure Cylinder structure Ball and stick structure Shape-determining forces 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 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 • 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. POSSIBLE SEQUENCE OF EVENTS IN FOLDING R HYDROPHOBIC COLLAPSE ↓ T E NUCLEATION(short range, ordered sec st) ↓ E A SUPERSECONDARY STRUCTURE ↓ R R STRUCTURAL DOMAINS ↓ T R FUNCTIONAL DOMAINS ↓ I A QUATERNARY (IF) ↓ A N PROSTHETIC GROUPS, PROCESSING(IF) ↓ R E ______ ACTIVITY Y -ΔG= (-9 TO -15) 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 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. metal ions • Several proteins can be complexed to a single metal ion that can stabilize protein structure by forming: • Covalent interaction (myoglobin-iron) • Salt bridges (carbonic anhydrase-zinc) 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 • 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. • 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. Properties of Proteins: Denaturation and Renaturation Denaturation • Denaturation is the disruption of the native conformation of a protein via breaking the noncovalent bonds that determine the structure of a protein • Complete disruption of tertiary structure is achieved by reduction of the disulfide bonds in a protein • The denatured protein loses its properties such as activity and become insoluble. Denaturing agents • Heat disrupts low-energy van der Waals forces in proteins • Extremes of pH: change in the charge of the protein’s amino acid side chains (electrostatic and hydrogen bonds). • Detergents: Triton X-100 (nonionic, uncharged) and sodium dodecyl sulfate (SDS, anionic, charged) disrupt the hydrophobic forces. • SDS also disrupt electrostatic interactions. • Urea and guanidine hydrochloride disrupt hydrogen bonding and hydrophobic interactions. • Reducing agents such as β-mercaptoethanol (β-ME) and dithiothreitol (DTT). • Both reduce disulfide bonds. Renaturation • Renaturation is the process in which the native conformation of a protein is reacquired. • Renaturation can occur quickly and spontaneously and disulfide bonds are formed correctly. • If a protein is unfolded, it can refold to its correct structure placing the S-S bonds in the right orientation (adjacent to each other prior to formation), then the correct S-S bonds are reformed. • This is particularly true for small proteins. Problem solvers: Chaperones • These proteins bind to polypeptide chains and help them fold with the most energetically favorable folding pathway. • Chaperones also prevent the hydrophobic regions in newly synthesized protein chains from associating with each other to form protein aggregates . Many diseases are the result of defects in protein folding. The problem of misfolding • When proteins do not fold correctly, their internal hydrophobic regions become exposed and interact with other hydrophobic regions on other molecules, and form aggregates. Outcome of protein misfolding • Partly folded or misfolded polypeptides or fragments may sometimes associate with similar chains to form aggregates. • Aggregates vary in size from soluble dimers and trimers up to insoluble fibrillar structures (amyloid). • Both soluble and insoluble aggregates can be toxic to cells. Prion disease • Striking examples of protein folding-related diseases are prion diseases, such as Creutzfeldt-Jacob disease (in humans), and mad cow disease (in cows), and scrapie (in sheep). • Pathological conditions can result if a brain protein known to as prion protein (PrP) is misfolded into an incorrect form called PrPsc. • PrPC has a lot of α-helical conformation, but PrPsc has more β strands forming aggregates. The prion protein • The disease is caused by a transmissible agent • Abnormal protein can be acquired by • Infection • Inheritance • Spontaneously Alzheimer’s Disease • Not transmissible between individuals • Extracellular plaques of protein aggregates of a protein called tau and another known as amyloid peptides (Aβ) damage neurons. Formation of plaques Quaternary structure What is it? • Aggregates are possible from dimer to dodecamers(12) or higher. • Each part of a protein with quaternary structure is called a subunit of that protein • Proteins are composed of more than one subunit. • They are oligomeric proteins (oligo = a few or small or short; mer = part or unit) • The spatial arrangement of subunits and the nature of their interactions. • Each polypeptide chain is called a subunit. • Proteins made of • Oligomeric proteins are made of multiple polypeptides that • One subunit = monomer • Two subunits: dimer • The simplest: a homodimer • Three subunits: trimer • Four subunit: tetramer are • identical → homooligomers (homo = same), or • different → heterooligomers (hetero = different) • Oligomer sometimes refers to a multisubunit protein composed of identical subunits, whereas a multimer describes a protein made of many subunits of more than one type. • The quaternary structure of a protein consists of the following characteristics of its subunits: 1. Their number 2. Their kind ; identical or non-identical primary structures 3. Their arrangement in three-dimensional space 4. the interactions between the subunits that stabilize the quaternary structure How are the subunits connected? • Sometimes subunits are disulfide-bonded together( membrane proteins), • most globular proteins , noncovalent bonds stabilize interactions between subunits (hemoglobin) • Many proteins that contain more than one chain are NOT said to have a quaternary st Complex protein structures Holo- and apo-proteins • Proteins can be linked to non-protein groups and are known as conjugated proteins. • When a protein is conjugated to a non-protein group covalently, the nonprotein group is known as a prosthetic group and the protein known as a holoprotein. • If the non-protein component is removed, the protein is known as an apoprotein. Others • Lipoproeins: Proteins associated with lipids • Phosphoproteins: proteins that are phosphorylated • Hemoproteins: proteins with heme • Nucleoproteins: proteins with a nucleic acid • Glycoproteins: proteins with carbohydrate groups Classes of glycoproteins • N-linked sugars • The amide nitrogen of the R-group of asparagine • O-linked sugars • The hydroxyl groups of either serine or threonine • Occasionally to hydroxylysine