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Vladimíra Kvasnicová
STRUCTURE OF PROTEINSSTRUCTURE OF PROTEINS
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The figure was adopted from: J.Koolman, K.H.Röhm / Color Atlas of Biochemistry, 2nd edition, Thieme 2005
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Syllabus of the lecture
• amino acids found in proteins
• peptides
• description of stucture of proteins
• classification of proteins
• physicochemical properties of proteins
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Chemical nature of proteins
• biopolymers of amino acids
• macromolecules (Mr > 10 000)
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
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Amino acids in proteins
L-αααα-aminocarboxylicacids
• 21 proteinogenic AAs
• other AAs are formed by a posttranslational modification
The figures were adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2
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The figure was found at http://www.imb-jena.de/~rake/Bioinformatics_WEB/gifs/amino_acids_chiral.gif (October 2007)
Amino acids belong amongoptical active
compounds
2 enantiomers : L- a D-
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The figure was adopted from http://webschoolsolutions.com/biotech/macro.htm (2006)
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The figure was adopted from http://webschoolsolutions.com/biotech/macro.htm (2006)
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Modified amino acids
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
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J.Koolman, K.H.Röhm / Color Atlas of Biochemistry, 2nd edition, Thieme 2005
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β-alanine γ-aminobutyric acid (GABA) taurine
J.Koolman, K.H.Röhm / Color Atlas of Biochemistry, 2nd edition, Thieme 2005
Nonproteinogenic amino acids
ornithine citrulline L-dihydroxyfenylalanine selenocysteine
(L-DOPA)
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Essential amino acids
• essential in a diet, they are not synthetized in a human body
1) branched chain AAs (Val, Leu, Ile)
2) aromatic AAs (Phe, Trp)
3) basic AAs (Lys, Arg, His)
4) Thr, Met
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Side chains of AAs determine final properties of proteins
Isoelectric point (pI)= pH value at which the net
charge of a compound is zero
pI = (pK COOH + pKNH3+) / 2
Solutions of AAs belong among ampholytes
(= ampho teric electrolytes ) „AMPHION “
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
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The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
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Absorption of UV radiation
• Tyr and Trp strongly absorb in 250 – 300 nm
→ spectrophotometric determination
Ability to bind other compounds
• Ser, Thr, (Tyr) ← phosphate or saccharide
• Asn ← saccharide
Formation of disulfide bonds (oxidation/reduction):
• 2 Cys-SH → Cys-S-S-Cys („cystine“)
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Peptides and proteins
• contain 2 or more AAs bound bypeptide bond(s)
• common names are used
• systematic names: AA1-yl -AA2-yl -AA3
oligo peptides: 2 – 10 AMK
poly peptides: >>>> 10 AMK
proteins: polypeptides of M r >>>> 10 000
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Examples of peptides
• hormones of hypothalamus (liberins and statins)
• hormones of hypophysis (STH, PRL, oxytocin, ADH)
• hormones of pancreas and GIT
• other hormones: calcitonin, parathyrin, natriuretic
peptides, angiotensins, somatomedins
• neurotransmitters and neuromodulators
(endorphins, enkephalins, substance P)
• cellular peptides (glutathione, carnosine, anserine)
• organoleptic peptides (Aspartam)
• toxins (snake and bee venoms)
• antibiotics (gramicidin, bacitracin)
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• border: polypeptide /proteinis not sharp (~ 50 AAs)
• AAs are bound by peptide bonds
• the order of AAs in a chain(= primary structure) is given by a genetic information
• the order of AAs is reportedfrom N- to C- terminal
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
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Description of structure of proteins
• the macromolecule contains various AAs ,in an exactly defined order and quantity
• spacial arrangement and biological functionare DEPENDENT
on the amino acid composition
• native protein ∼∼∼∼ biological active conformation
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side chains of AAs influence a finalstructure of proteins
The figure was adopted from http://fig.cox.miami.edu/~cmallery/255/255prot/fig5x5.jpg (2007)
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• the peptide chain has a special
space arrangement:
• only some proteins are composed of subunits (= quaternary structure)
The figure was adopted from Albert L. Lehninger et al.: Principles of Biochemistry, ISBN 0-87901-500-4
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Bonds found in proteins
1) covalent� peptide bond -CO-NH-
� disulfide bond -S-S-
2) noncovalent interactions� hydrogen bonds -H.....O- -H.....N-
� hydrophobic interactions nonpolar side chains
� ionic interactions -COO- / +H3N-
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Primary structure of proteins
= order of amino acids
• read: from N - to C- end
• it is coded on a genetic level
• stabilization :peptide bonds
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
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Secondary structure of proteins
= spatial arrangement of the polypeptide chain given by rotation of the planar peptide bonds aroundαααα-carbons
stabilization :hydrogen bonds
between –CO - and -NH-of the peptide bonds
real proteins : different parts of the polypeptide chain exist in various secondary structures
The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/sf3x10b.jpg (October 2007)
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The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x20.jpg (October 2007)
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Helical structure (helix)• various types of the spiral:
different steepness, direction of rotation,
number of AAs per turn
• peptide bond planes are parallel
to the axis of the helix with R-
perpendicular to it
• H-bonds are formed between AAs found
above and below themselves
the most common :
� αααα-helix (right-handed)
� collagen helix (left-handed, steeper)
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
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ββββ-pleated sheet ( ββββ-structure)
• direction of parts of the
polypeptide chain is either
parallel or antiparallel
N → C N → C
N → C C → N
• R- are placed above or
below the plane of the sheet
• H-bonds are formed between peptide bonds of the
neighboring parts of the polypeptide chain
• it brings strength to proteins The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss,
Inc., New York, 1997. ISBN 0-471-15451-2
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ββββ-bend (reverse or ββββ-turn)
• reverse the direction of a polypeptide chain, helpi ng
it form a compact, globular shape
• often connect successive strands of antiparallel
sheets
Nonrepetitive secondary structure
• loop or coil conformation
• not random but less regular structure than αααα- or ββββ-
• one half of a protein molecule exist in it
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αααα-helix
ββββ-sheet
motif :barrel
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2
supersecondary structures: „motifs“
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zinc finger
leucine zipperMotifs of proteins interacting
with DNA
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Tertiary structure of proteins
= spatial arrangement of the secondary
structures (folding of domains)
stabilization: between side chains of AAs
1) hydrogen bonds
2) ionic (electrostatic) interactions
3) hydrophobic interactions
4) disulfide bonds
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tertiary structure
secondary structuresThe figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x20.jpg (October 2007)
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a function is related to the spatial structure
IT DEPENDS ON AMINO ACIDS COMPOSITION
funkční domény
The figure was adopted from http://fig.cox.miami.edu/~cmallery/255/255prot/ecb4x19.jpg (October 2007)
functional domains
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Classification of proteins according to their tertiary structure
1) globular proteins (spheroproteins)
� spheroidal shape
� both secondary structures are abundant
2) fibrous proteins (scleroproteins)
� rod-like shape
� one secondary structure predominates
� e.g. αααα-keratin, collagen
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Quaternary structure of proteins
= oligomeric structure of a protein (2 or more
subunits ~ monomers)
• i.e. the structure is found only in proteins
composed from 2 or more chains (subunits)
• stabilization: noncovalent interactions
• the proteins have an „allosteric effect“
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The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x23.jpg (October 2007)
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SUMMARYof protein structure description
The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x24.jpg (October 2007)
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protein must be properly folded
NATIVE PROTEINThe figure was adopted from Alberts, B. a kol.: Základy buněčné biologie. Úvod do molekulární biologie buňky. Espero Publishing,
s.r.o., Ústí nad Labem, 1998. ISBN 80-902906-0-4
unfolded protein
folded protein
FOLDINGactive site
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J.Koolman, K.H.Röhm / Color Atlas of Biochemistry, 2nd edition, Thieme 2005
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Classification of proteins
1) by localization in an organism
� intra- / extracellular
2) by function
� structural / biological active
3) by shape
� globular / fibrous
4) by chemical composition
� simple / complex (conjugated) proteins
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→ conjugated proteins contain polypeptide chain
(= apoprotein) + nonprotein prosthetic group
� glycoproteins
� metalloproteins
� hemoproteins
� phosphoproteins
� nucleoproteins
The figure was adopted from http://connection.lww.com/Products/porth7e/documents/Ch24/jpg/24_002.jpg (October 2007)
� (lipoproteins: lipids are not covalently bound to proteins)
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Physicochemical properties
• water solubility depends on the structure
• proteins form colloidal solutions(viscosity, sedimentation, light dispersion)
colloidal-osmotic pressure = onkotic pressure
• proteins can be salting-out of the solution(~ water sheet removing)
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• proteins can be denaturated
� heat, whipping, shaking, radiation
� strong pH changes, salt of heavy metals, organic solvents, detergents
The figure was adopted from http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05-06_denaturation_1.jpg (October 2007)
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• proteins act as antigens formation of antibodies
• proteins give positive reaction with biuret reagent
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• proteins strongly absorb UV radiation
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• proteins are ampholytes
-COOH -COO- + H+
-NH2 + H+ -NH3+
under physiological pH
proteins are negatively charged
ANIONS
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Determination of proteinsin a laboratory
• chemical reacion of peptide bonds with biuret reagent - spectrophotometry
• complementary reaction with an antibody - immunochemistry
• separation in an electric field- electrophoresis
• denaturation
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Recommended literature
http://www.megabooks.cz/prodejny/academic-bookshop/praha/kontakt/