Protein structure

BIOMEDICAL IMPORTANCE Protein function – Catalyze metabolic reactions – Power cellular motion – Provide structural integrity Defect in protein maturation – Genetic or nutritional Creutzfeldt- Jakob disease, scrapie, Alzheimer’s disease, and bovine spongiform encephalopathy (mad cow disease). Scurvy

BIOMEDICAL IMPORTANCE Defect in primary structure – Sickle cell the structure of a protein provides insight into how it fulfills its functions.

Configuration – the geometric relationship between a given set of atoms – configurational alternatives requires breaking covalent bonds Conformation – the spatial relationship of every atom in a molecule.

Classification of proteins Solubility, shape, or the presence of nonprotein groups. Solubility – Soluble At physiologic pH and ionic strength – Integral membrane proteins Shape – Globular proteins Most enzymes – Fibrous proteins Many structural proteins

Classification of proteins Nonprotein groups – Lipoproteins – Glycoproteins – Hemoproteins Myoglobin, hemoglobin, cytochromes – Metalloproteins Classification based on homology – Sequence & structure.

THE FOUR ORDERS OF PROTEIN STRUCTURE Primary structure – the sequence of the amino acids in a polypeptide chain Secondary structure – The folding of short (3- to 30-residue),contiguous segments of polypeptide into geometrically ordered units

Tertiary structure – the three-dimensional assembly of secondary structural units Quaternary structure – the number and types of polypeptide units of oligomeric proteins

Secondary structure the two most common types, – α-helix – β-sheet The Alpha Helix – The R groups, face outward – right-handed – Represent as cylinders

The stability – Hydrogen bonds – proline disrupts the conformation of the helix

Hydrogen bonds

The Beta Sheet Zigzag or pleated pattern Highly extended Stability from hydrogen bonds – Between segments, or strands, of the sheet Parallel β sheet – in the same direction amino to carboxyl Antiparallel sheet Represents β sheets as arrows – amino to carboxyl

Antiparallel β sheet parallel β sheet

Loops & Bends Turns and bends – Short segments of amino acids that join two units of secondary structure – Proline and glycine often are present in β turns. Loops – Much Longer than turn & bends – serve key biologic roles Participate in catalysis

A β-turn that links two segments of antiparallel β sheet

Loops & Bends Helix-loop-helix motifs – binding portion of DNA binding proteins repressors & transcription factors many loops and bends reside on the surface of proteins – Epitopes lack apparent structural regularity Stabilized through – hydrogen bonding, salt bridges, and hydrophobic interactions

Disordered regions – at the extreme amino or carboxyl terminal – High onformational flexibility – ligand-controlled switches

Tertiary Structure the entire three dimensional conformation of a polypeptide Domains – Assembly of secondary structures Helices, sheets, bends, turns, and loops – a section of protein structure sufficient to perform a particular chemical or physical task Binding to ligand – Single/multiple domains

Examples of tertiary structure of proteins A single -domain structure

Two-domain structure

Quaternary structure assembled from more than one polypeptide, or protomer Monomeric Dimeric – Homodimers – Heterodimer Greek letters (α, β, γ etc) are used α 2 β 2 γ (five subunits of three different types)

FACTORS STABILIZE TERTIARY & QUATERNARY STRUCTURE Noncovalent interactions – hydrophobic interactions Interior of the protein – Hydrogen bonds and salt bridges – Individually weak Covalent – disulfide (S-S) bonds – Intrapolypeptide – Interpolypeptide

Techniques Study of higher orders of protein structure – X-ray crystallography, NMR spectroscopy, THREE-DIMENSIONAL STRUCTURE analytical ultracentrifugation Gel filtration Gel electrophoresis

Techniques Mass spectrometry – A tool for determining primary structure and for the identification of posttranslational modifications. DNA cloning Genomics – Increases the speed and efficiency for determination of primary structures of proteins.

Proteome – to determine the primary sequence and functional role of every protein expressed in a living cell

PROTEIN FOLDING Occurs via a stepwise process – Short segments fold into secondary structural units that provide local regions of organized structure

Denatured (Unfolded) – treatment with acid or base, chaotropic agents, or detergents – Aggregates disordered complexes of unfolded or partially folded polypeptides held together by hydrophobic interactions Auxiliary Proteins Assist Folding – Chaperones Hsp70 – Prevent aggregation

Operate in – Folding – Unfolding Protein Disulfide Isomerase – Catalyzing disulfide exchange Rupture & reformation Proline-cis,trans-Isomerase – Particularly common in β-turns

SEVERAL DISEASES RESULT FROM ALTERED PROTEIN CONFORMATION NEUROLOGIC DISEASES – Prion diseases Creutzfeldt-Jakob disease, scrapie α-helical structure to the β-sheet structure – Alzheimer’s Disease Diseases of collagen maturation – Ehlers-Danlos syndrome – Scurvy

Summary Proteins may be classified on the basis of – the solubility, – Shape, – Function, – the presence of a prosthetic group Such as heme Proteins perform complex physical and catalytic functions

Primary structure – The gene-encoded sequence of amino acids. – Stabilized by covalent peptide bonds Secondary structure results from – folding of polypeptides into hydrogen-bonded motifs such as the α helix, the β-pleated sheet, β bends, and loops. Supersecondary motifs – Combinations of these motifs

Tertiary structure – the relationships between secondary structural domains. Quaternary structure – Proteins with two or more polypeptides (oligomeric proteins)