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 OFPROTEIN 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

• 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 • α2β2γ (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)