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Chymotrypsin (247 aa)

Conformation: the spatial arrangement of atoms in a protein.
Among the many conformations that are theoretically possible in a
protein, one (or a few) conformation exists in biological system.
Native conformation: the conformation of the functionally active
protein.

Levels of structure in proteins

The primary structure describes mainly the sequence of amino acid residues in the polypeptide chain. It describes all covalent bonds (peptide bonds and disulfide bonds) linking amino acid residues in a polypeptide chain. A chain B chain .

Secondary structure refers to particularly stable arrangements of amino acid residues. Most important secondary structures are: • α helix • β sheet • β turn • Ω loop . near one another in the linear sequence (primary structure). These spatial arrangements are local and give rise to regular repeating structures.

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youtube.Hydrogen bonding for an α helix involve N-H and C=O groups of peptide bonds The CO group of residue i forms a hydrogen bond with the NH group of residue i + 4 http://www.com/watch?v=eUS6CEn4GSA&feature=related .

Structure of a β strand  amino acid residues are almost completely extended.5 Å.  the side chains of adjacent residues point in opposite directions. .  the distance between two adjacent residues is 3.

Antiparallel β sheet: adjacent β strands run in opposite directions Hydrogen bonds connect each amino acid on one strand to a single amino acid on the adjacent strand. .

http://www.com/watch?v=wM2LWCTWlrE&NR=1 .youtube.Parallel β sheet: adjacent β strands run in the same direction Hydrogen bonds connect each amino acid on one strand with two different amino acid on the adjacent strand.

Voet.W.G.Connections between adjacent strands in β sheets D. Zanichelli Editore S.p. Copyright © 2007 . Pratt. C. J. Voet.A. FONDAMENTI DI BIOCHIMICA 2/E.

.β turns: connecting elements linking secondary structures A peptide bond involving proline in the cis configuration is prone to a tight turn.

periodic structures Figure 6-12 .X-ray structure of carboxypeptidase A Loops do not have regular.

. It is the three dimensional structure of the functionally active protein (native conformation).The tertiary structure refers to the overall three dimensional arrangement of all atoms in a protein.

immunoglobulins. keratin. proteins are grouped in: fibrous proteins globular proteins shape: one preferred direction spherical. hemoglobin .Based on tertiary structure. elastin enzymes. some hormones. globular secondary structures: single (few) type(s) several types water solubility: insoluble soluble sensitivity to proteases: very low high function: structural dynamic examples: collagen.

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Zanichelli editore S.A. Copyright © 2007 .p. BIOCHIMICA 6/E.Leucine zipper Berg et al..

Globular proteins are compact structures (human serum albumin 585 res.) .

Tertiary structure of myoglobin (153 res.) .

Myoglobin three dimensional view Yellow: hydrophobic amino acids Blue: charged amino acids White: other amino acid. cross sectional view .

Glu. buried to the solvent: Val.In globular proteins amino acid residues are distributed according to the polarity of their side chains: • in the protein core. • on the protein surface interacting with the solvent: Arg. His. . Asn. • on the protein surface. Met and Phe. Ile. Thr. Tyr. but also inside: Ser. Leu. Asp. Gln. Lys.

Supersecondary structures (motifs): combinations of secondary structural elements. βαβ motif β hairpin motif αα motif .

binding of small molecules.e. interaction with other proteins).e.Domains : a) distinct structural units of a polypeptide. c) may have separate functions (i. by proteolysis). . b) may fold as independent compact units. They maintain their structure when separated from the rest of the protein (i.

W.Glyceraldehyde-3phosphate dehydrogenase in red: domain that bind NAD in green: domain that bind glyceraldehyde-3phosphate D. Zanichelli Editore S. Copyright © 2007 . C. J. Voet. Voet.p.G.A. FONDAMENTI DI BIOCHIMICA 2/E. Pratt.

α β α β .Quaternary structure: the three-dimensional structure of a multi-subunit protein and how the subunits fit together.