Protein Structure PDF

Introduction to Protein Structure All the Information is coded!!!! Genome Transcriptome Proteome Metabolome From “genome” to “proteome” The ultimate coded information needs to be DECODED!!! The CODON table Amino acids: the fundamental building blocks Alan...

Introduction to Protein Structure All the Information is coded!!!! Genome Transcriptome Proteome Metabolome From “genome” to “proteome” The ultimate coded information needs to be DECODED!!! The CODON table Amino acids: the fundamental building blocks Alanine A Methionine M Cysteine C Asparagine N Aspartic Acid D Proline P Glutamic Acid E Glutamine Q Phenylalanine F Arginine R Glycine G Serine S Histidine H Threonine T Isoleucine I Valine V Lysine K Tryptophan W Leucine L Tyrosine Y Amino Acids  Backbone and side chain All amino acids have a common part: the backbone Each amino acid type has a different side chain The Cα atom connects the backbone and the side chain The first carbon atom in the side chain is called Cβ (except for Gly) Only 20 amino acids are responsible for all the protein structures found in Nature!!!  Proteins 1) An important class of biological macromolecules present in all organisms 2) They regulate most of the biological activities 3) Also known as a polypeptide chain of amino acids 4) To be biologically active, proteins adopt specific three-dimensional folded structure  Protein Structure: Introduction Different amino acids have different properties These properties will affect the protein structure and function Hydrophobicity, for instance, is the main driving force (but not the only one) of the folding process  Protein structure: overview Structural element Description Primary structure amino acid sequence of protein Secondary structure helices, sheets, turns/loops Super-secondary structure association of secondary structures Domain self-contained structural unit Tertiary structure folded structure of whole protein includes disulfide bonds Quaternary structure assembled complex (oligomer) homo-oligomeric (1 protein type) hetero-oligomeric (>1 type)  Hierarchy of protein structure Primary Structure = Sequence of amino acids MKYNNHDKIRDFIIIEAYMFRFKKKVKPEVDMTIKEFILLTYLFHQQENTL PFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQRE KIAERVTLFDQIIKQFNLADQSESQMIPKDSKEFLNLMMYTMYFKNIIKK HLTLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYL IKERSTEDERKILIHMDDAQQDHAEQLLAQVNQLLADKDHLHLVFE Secondary Structure Tertiary Local Interactions Global Interactions Protein Structure Hierarchy Quaternary Tertiary Structure Structure Secondary Structure Primary structure Primary structure ✔ 1D representation of Protein: PRIMARY STRUCTURE, also known as the protein “amino acid sequence”. Hemoglobin amino acid sequence : MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKK VLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAG VANALAHKYH From where did we retrieve this sequence??? Protein structure How amino acids form protein structure? Protein form structures when amino acids form “peptide bonds” to connect to each other. Formation of a Peptide Planarity of Peptide (Amide) Bond cis and trans Isomers The trans isomer is generally more stable because of steric crowding of side chains in the cis isomer. Secondary Structure ✔ The primary amino acid sequence gives rise to the secondary structure of a protein Alpha helix Beta sheets Loops and Coils How are these structures stabilized??? ✔ Linus Pauling, the Nobel prize winner in Chemistry, 1954 (and later Peace) predicted the alpha helical pattern from theory. ✔ He is credited with the very successful prediction that protein structure is based on HYDROGEN BONDS. ✔ He assumed 100% hydrogen bonding between amino and carboxyl groups on the main chain He predicted the shape and size of the helix exactly as shown later by experimental studies on Keratin, a protein which is almost pure alpha-helix!!!! Linus Pauling 1901-1904  Alpha helix ✔ The alpha helix has 3.6 amino acids/turn, hydrogen bonds which run almost exactly parallel to the helix axis. ✔ Hair consists of almost pure alpha-helix as the protein keratin. ✔ Many ion channels are composed of alpha helices. ✔ Important amino acids involved: hydrophobic and charged. Important amino acids- MALEK. Proline and Glycine have lower propensities in alpha helices. Always right- handed helices Alpha helices may contain 4-40 amino acids Average no of amino acids/ helix is ten, equivalent to three turns The rise per residue is 1.5 Å Basis for the helical dipole In an alpha helix all of the peptide dipoles are oriented along the same direction. Consequently, the alpha helix has a net dipole moment. The separation of charge in a molecule determines its dipole moment (µD= Z.d). One electron unit of charge separated by 1Å gives a dipole moment of 4.8 Debys units. Since the dipole moment of a peptide bond is 3.5 Debye units, the alpha helix has a net macro dipole of: n x 3.5 Debye units (where n= number of residues) This is equivalent to 0.5 – 0.7 unit charge at the end of the helix. The Helix Macro-Dipole The amino terminus of an alpha helix is positive and the carboxy terminus is negative. Beta sheet ✔ Beta sheets consist of individual beta strands. ✔ The beta strands are connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. ✔ Beta sheets are seen in common structural motifs like Greek key motif, β-α-β motif. ✔ Important amino acids involved: Tyr, Phe and Trp and β-branched amino acids (Thr, Val, Ile).  Random Coils and Loops ✔ Present on the surface of structure and interact with the surroundings. ✔ No constraints ✔ Amino acid substitutions, insertions and deletions more. ✔ Usually components of active sites ✔ Tend to have polar and charged amino acids.  Amino acids α-helix β-strand turns 1 Glu 1.59 0.52 1.01 2 Ala 1.41 0.72 0.82 3 Leu 1.34 1.22 0.57 4 Met 1.30 1.14 0.52 5 Gln 1.27 0.98 0.84 6 Lys 1.23 0.69 1.07 7 Arg 1.21 0.84 0.90 8 His 1.05 0.80 0.81 9 Val 0.90 1.87 0.41 10 Ile 1.09 1.67 0.47 11 Tyr 0.74 1.45 0.76 12 Cys 0.66 1.40 0.54 13 Trp 1.02 1.35 0.65 14 Phe 1.16 1.33 0.59 15 Thr 0.76 1.17 0.90 16 Gly 0.43 0.58 1.77 17 Asn 0.76 0.48 1.34 18 Pro 0.34 0.31 1.32 19 Ser 0.57 0.96 1.22 20 Asp 0.99 0.39 1.24  Favoring Indifferent Non-favoring α-helix Ala, Leu, Met, His, Val, Ile, Phe, Trp. Tyr, Thr. Gly, Ser. Pro Glu, Gln, Lys, Cys Asp, Asn, Arg β-strand Val, Ile, Phe, Trp, Ala, Leu, Met, His, Glu, Gln, Lys, Asp, Tyr, Thr Gly, Ser, Arg Asn, Pro, Cys Reverse Gly, Ser, Asp, Asn, Gln, Lys, Tyr, Thr, Ala, Leu, Met, His, turns Pro Arg Val, Ile, Phe, Trp, Cys, Arg http://www2d.biglobe.ne.jp/~chem_env/amino/amino2j_e.html Protein Structure: Ramachandran plots Psi (ψ) The backbone of a residue is characterized by two angles: psi and phi. Phi (Φ) φ (phi): around the α-carbon—amide nitrogen bond ψ (psi): around the α-carbon—carbonyl carbon bond Can they take any value? Fortunately not This effect was studied long ago by GN Ramachandran He proposed a diagram to visualize these angles (phi in the X axis, psi in the Y axis) of amino acid residues  Ramachandran plot Phi (Φ) and Psi (ψ) rotate, allowing the polypeptide to assume its various conformation no steric Some conformations of the clashes polypeptide backbone result in steric hindrance and are disallowed Glycine has no side chain and is therefore conformationally highly permitted flexible (it is often found in turns) if atoms are more closely Different types of secondary spaced structure are clustered in different regions of the diagram G.N. Ramachandran, C. Ramakrishnan, V. Sasisekharan - Stereochemistry of polypeptide chain configurations: JMB (1963) 7(1) 95-99 G.N. Ramachandran and V. Sasisekharan Conformation of Polypeptides and Proteins: Advances in Protein Chemistry (1968) 23, 283-437  Phi & Psi angles for Regular Secondary Structure Conformations Structure Phi (φ) Psi(ψ) Anti-parallel β-sheet -139 +135 Parallel β-Sheet -119 +113 Right-handed α-helix -57 -47 310 helix -49 -26 π helix -57 -70 Polyproline I (cis) -83 +158 Polyproline II (trans) -78 +149 Polyglycine II -80 +150 Rotational constraints emerge from interactions with bulky groups (i. e. side chains). Phi & Psi angles define the secondary structure adopted by a protein. Tertiary structure ✔ Secondary structures “fold” to form the tertiary structures of a protein: 3-dimensional arrangement of protein in space. ✔ Protein folds by hydrophobic interactions ✔ Specific tertiary interactions: salt bridges and disulfide bonds Myoglobin Sucrose porin Protein Kinase C Quaternary structure ✔ Many polypeptide chains interact to form different chains to form a single protein. For example, Hemoglobin has two polypeptide chains A and B. Quaternary structure Hemoglobin Protein motif and domains DOMAIN: ✔ A part of structure that can fold irrespective of the presence of other segments of the chain. ✔ A single protein can be composed of several domains. MOTIF: Structural motifs are a combination of conserved secondary structure elements that may be present in proteins with no evolutionary relationship. Domains are functional structural regions while motif represents only a structural region may not be associated with any function. Examples of Domains: Leucine Zipper Domain Zn finger DNA binding domain Examples of Motifs: Helix loop helix Greek key motif Beta hairpin  Protein folding Proteins tend to fold into the lowest free energy conformation. The folding process of a protein involves several steps: ❖ The protein creates some patterns due to local interactions with the closest residues in the chain. These patters are called the protein secondary structure ❖ Afterwards, the secondary structure motifs organize into stable patterns, called tertiary structure ❖ Finally, proteins can be composed of several subunits or monomers  Protein Folding Proteins tend to fold into the lowest free energy conformation. Proteins begin to fold while the peptide is still being translated. Proteins bury most of its hydrophobic residues in an interior core to form an α helix. Most proteins take the form of secondary structures α helices and β sheets. Molecular chaperones, hsp60 and hsp 70, work with other proteins to help fold newly synthesized proteins. Much of the protein modifications and folding occurs in the endoplasmic reticulum and mitochondria. Why Bioinformatics as a tool in Proteomics?? No. of Protein Structures Challenges in the No. of Protein field of proteomics: Sequences ✔ Data Deluge: Big Data Analysis ✔ Sequence-Structure Gap ✔ Protein folding Sequence-Structure Space Bioinformatics and Proteomics Protein Databases ✔ Sequence Databases ✔ Uniprot Check for yourself the sequence-structure space!!!! ✔ SwissProt ✔ TrEMBL File Formats: Fasta, ASN.1, EMBL, Genbank, PIR ✔ Structure Databases ✔ RCSB Protein Data Bank (PDB) File format : PDB From Sequence to Secondary Structure “Prediction” MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPW TQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLA HLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLA HHFGKEFTPPVQAAYQKVVAGVANALAHKYH Helix? Beta sheets? Coils? Secondary Structure Prediction ✔ Available Servers: PSIPRED, Jpred, PredictProtein  Domain and Motif Prediction MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPW TQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLA HLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLA HHFGKEFTPPVQAAYQKVVAGVANALAHKYH Protein family and domain Search ✔ Available Servers: InterPro, ScanProsite Tertiary Structure Prediction ✔ Homology Modeling ✔ Ab-initio Modeling SCIENCEISANART No 3D structure available Unknown 3D protein sequence: Target/Query Sequence BLAST Search for templates in protein structure database for “homologous” structures. If structure found Align target sequence with template sequence Build Model Validate it Homology modeling SCIENCEISANART No 3D structure available Unknown 3D protein sequence: Target/Query Sequence BLAST Search for templates in protein structure database for “homologous” structures. NO structure found!!! Threading or Ab-initio modeling Visualization tools ✔ Pymol ✔ Visual Molecular Dynamics ✔ Chimera Representation of 3D structures Atomic details (Protein Data Bank) Ball and stick model Ribbon model Space filling models Van der Waals radii Occupy space & molecular surfaces (Courtesy of MolViz)