Protein Structure Lecture (15) PDF

Lecture (15) Protein structure  Secondary structures  It is the local arrangement of the backbone of a small part of polypeptide (localized organized structure of amino acids that are next to each other). - It is stabilized by hydrogen bonding between backbone atoms. -...

Lecture (15) Protein structure  Secondary structures  It is the local arrangement of the backbone of a small part of polypeptide (localized organized structure of amino acids that are next to each other). - It is stabilized by hydrogen bonding between backbone atoms. - Again, hydrogen bonding occurs between peptide bonds in the backbone (not R-groups) with amide NH being donor and CO being acceptor. - The two bonds within each amino acid residue freely rotate: 1) Bond between the α-carbon and amide nitrogen. 2) Bond between the α-carbon and carbonyl carbon. Regular secondary structures 1) α- helix  The helix has an average of 3.6 amino acids per turn.  Pitch : linear distance between corresponding points on successive turns = 5.4 Å.  α-helix is very stable because of the linear hydrogen bonding.  Trans R-groups of amino acids project outward from helix → avoiding steric hindrance.  Amino acids not found in α-helix : ‫مهم جدا‬ 1) Glycine: too small. 2) Close proximity of a pair of charged amino acids with similar charges (repulsion). 3) Amino acids with branches at the β-carbon (valine, threonine, and isoleucine). 4) Proline: ‫المخرب األعظم‬ - No rotation around N-α C bond (rigid). - No hydrogen bonding of α-amino group. - Proline is usually found at end of α-helix or β-strands to break the smoothness of the pattern by creating kinks. 2) β-pleated sheet ‫الورقة المتعرجة‬  It composed of two or more straight chains called β strands that are hydrogen bonded side by side : - Typically, β-sheet contains 4 or 5 β-strands (sometimes, 10 or more).  Optimal hydrogen bonding occurs when sheet is bent or zigzag (pleated).  β sheets can be classified according to direction (from N to C): A. Purely parallel: - Each amino acid H- bonds to 2 amino acids surrounding the one opposite to it (2:1 ratio). B. Purely antiparallel. - Each amino acid H- bonds to 1 amino acid opposite to it (1:1 ratio). - More stable due to pattern of hydrogen bonding (perpendicular to backbone or straight). C. Mixed.  Effect of amino acids : A. Proline disrupts β strands.‫غير مستحب‬ B. Amino acids with branched β-carbon (valine, threonine and Isoleucine) and large aromatic amino acids (phenylalanine, tryptophan, and tyrosine) are more present in β-sheets. ‫مسموحين‬  Non-regular secondary structures 1) β-turns (hairpin bend)  They are compact, regular U-shaped secondary structures. ‫مثل دبوس الشعر‬  They are used to connect main secondary structures, especially when there is a sharp change in direction.  They are composed of 4 amino acids : A. H-bonding between 1 and 4 is responsible for stability. B. Proline is commonly present at position 2 (creates a kink). C. Glycine is commonly found at position 3 (small and can fit). 2) Loops and Coils  Flexible, irregular structures that connect main secondary structures : - Ill-defined with no constant pattern → amino acids are often not conserved. ‫ال يوجد أحماض أمينية ثابتة‬ - They contain polar residues → found on surface of protein where they provide flexibility. Super-secondary structures  Regions in proteins that contain an ordered organization of secondary structures.  Types include motifs (modules) ‫ تركيبات بنائية صغيرة‬and domains ‫تركيبات وظيفية كبيرة‬  1) Motifs (modules)  Multiple repeated consecutive secondary structures → organized into larger motifs that can be part of domains. ‫يجب أن يكونوا متتاليين‬  Usually constitutes small portion of protein (typically less than 20 amino acids).  In general, motifs may provide us with information about the folding or structure of proteins, but not biological function.  Examples of structural motifs : A. Helix-loop-helix: found in many proteins that bind DNA. B. Helix-turn-helix: also capable of binding DNA. C. Immunoglobulin (antibody) fold or module: enables interaction with antigens or foreign bodies of various structures and sizes (more complex motif) : - It is a more complex motif consisting of β-strand – loop – β-strand – loop……  Tertiary structure  Different definitions : - Overall conformation of 1 polypeptide chain. - 3-D arrangement of all amino acids residues in 1 polypeptide. - Spatial arrangement of all amino acid residues that are far apart in the sequence. - Arrangement and interactions of R-groups that are far apart in 1 polypeptide. - For proteins consisting of only 1 polypeptide, it is the final conformation of protein. Shape-determining forces of tertiary structure  Shape of tertiary structure is determined mainly by non-covalent forces between the R- groups: 1) Hydrophobic interactions: - They are probably the most important shape-determining force. - A system is more thermodynamically (energetically) stable when hydrophobic groups are clustered together rather than extended into the aqueous surroundings. - So, when translation occurs in aqueous cytosol → hydrophobic amino acids will cluster and aggregate → they hide inside the core of protein away from water. - So, in general, hydrophobic amino acids are located inside globular proteins, while hydrophilic amino acids are located on surface of protein. - However, polar amino acids can be located in the interior and non-polar can be located on the exterior as long as they have important structural or functional roles. - When polar amino acids are found inside, they form hydrogen bonds to other amino acids or to backbone. 2) Van der Waals interactions: - They are weak and transient, because they depend on rapid electron cloud movements. - Both attractive and repulsive van der Waals forces control protein folding. - Although van der Waals forces are extremely weak, they are significant because there are so many of them in large proteins. 3) Hydrogen bonds (dipole-dipole): - Occur between polar R-groups and between polar R-groups with surrounding aqueous medium (serine with asparagine, serine with water…..). 4) Charge-charge (salt bridges, ionic, electrostatic ): - Occur between oppositely charged R- groups of amino acids. - Occurs between any positive (arginine, lysine, Histidine) with any negative (glutamic or aspartic). 5) Charge-dipole interactions between charged R groups with the partial charges of water : - Notice that same charged group can form either hydrogen bonding or electrostatic interactions.  Stabilizing factors  There are two forces that don’t determine 3-D structure of proteins, but stabilize structure: ‫ال يحددوا الشكل ولكن يثبتوه بعد أن يتحدد بالروابط الالتساهمية‬ 1) Disulfide bonds: - R-group of cysteine contains a reactive sulfhydryl group (SH), which can be oxidized to disulfide bond (S—S) with a second cysteine. - Crosslinking of two cysteines form a new amino acid called cystine. - Disulfide bond is the only covalent bond between R-groups in the tertiary structure. 2) Metal ions :  Some proteins can be complexed to a single metal ion that can stabilize protein structure by forming: 1) Covalent interaction with R-groups (Fe in myoglobin and hemoglobin). 2) Salt bridges (Zn in carbonic anhydrase).  Please remember that proteins are not static: they are always moving and shaking. How to look at proteins ?