Download Protein structure

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
• 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)