COURSE MATERIAL :- PRINCIPLES of PROTEIN STRUCTURE

last modified 9/12/94

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INTRODUCTION

OVERVIEW OF PROTEIN SYNTHESIS

PRIMARY STRUCTURE OF PROTEINS

PROTEIN GEOMETRY

OVERVIEW OF MOLECULAR FORCES

SECONDARY STRUCTURE

SUPER-SECONDARY STRUCTURE

TERTIARY STRUCTURE

PROTEIN FOLDS

QUATERNARY STRUCTURE

PROTEIN INTERACTIONS

SUMMARY

This is only a first attempt at the `fleshing out' process; any contribution
or comment is very welcome, constructive or otherwise. - Alan Mills   13/10/94
______________________________________________________________________________
see also URLs	http://www.cryst.bbk.ac.uk/education/PPS.html
	    &   http://seqnet.dl.ac.uk:8000/vsns-pps/consult/sept30.html
______________________________________________________________________________

                     THE PRINCIPLES OF PROTEIN STRUCTURE

INTRODUCTION
	-Prerequisites
	-Objectives & Assessment
	-Course	Map, or Contents Page (this page HTMLised?)

OVERVIEW OF PROTEIN SYNTHESIS
	-Cellular Organisation
	-Transcription
	-Translation
	-Post-translational processing
	-Transport
        -Degradation

PRIMARY STRUCTURE OF PROTEINS
	-Nomenclature (Genetic & Single-Letter Codes)
	-Databases
	-The Amino Acids & Their Properties 
	 	0.Chemical Structure	
		 1.Size 
		 2.Charge 
		 3.Hydrophobic 
		 4.Aromatic 
		 5.Polar
 	-Chirality
	-The Disulphide Bond

PROTEIN GEOMETRY
	-Nomenclature
	-The Peptide Bond
	-Torsion Angles 1.Main Chain phi/psi
	-Torsion Angles 2.Side Chain Rotamers
        -Ramachandran Plot

OVERVIEW OF MOLECULAR FORCES
        -Covalent Bonds; Lengths and Angles (& distortions thereof)
	-Van der Waals Forces
	-Hydrogen Bonds
	-Electrostatic Effects, Salt Bridges
	-The Hydrophobic Effect
	-The Importance of Solvent
	-Overall Energetics, Stability, & Energy Minimisation

SECONDARY STRUCTURE
	-General, including representations, CD, prediction etc
	-The Alpha Helix 1.
	-The Alpha Helix 2.
	-Beta Sheets 1.Parallel
	-Beta Sheets 2.Anti-Parallel
	-Beta Sheets - General
 	-Turns
	-`Random' Coil

SUPERSECONDARY STRUCTURE  (amendment to first draft)

TERTIARY STRUCTURE
	-Globular (mainly enzyme) vs Fibrous, Structural, and Membrane Proteins
        -Folds; classification and representation
	        1.All alpha
		2.All beta
		3.Wound alpha/beta, and variations
		4.Mixed alpha+beta
	-Domains 
	-Mosaic Proteins
	-Interactions among Proteins (receptors, carriers, Igs, hydrolases, etc)

FOLDS (amendment to second draft)

QUATERNARY STRUCTURE
	-Dimers, Trimers, Tetramers & +
	-Cooperativity, Allosteric Effects
	-Conformational Changes (related to function, regulation?)
	-Multi-enzyme complexes, Chaperonins, Cellular `Machinery'
	-Families and Superfamilies
	-Functional Groupings

PROTEIN INTERACTIONS  (amendment to first draft)

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This is only a second attempt at the `fleshing out' process; any contribution
or comment is very welcome, constructive or otherwise. - Alan Mills   13/10/94
........................................and subsequently  on 24th.October 1994
........................................and then marked up on 21st.November1994
______________________________________________________________________________
see also URLs	http://www.cryst.bbk.ac.uk/education/PPS.html
	    &   http://seqnet.dl.ac.uk:8000/vsns-pps/consult/sept30.html
______________________________________________________________________________

THE PRINCIPLES OF PROTEIN STRUCTURE

INTRODUCTION

-Prerequisites
as PMR has previously listed, plus any amendments. We may cite references for those who need a little revision. Such stuff may be sent to students pre-registering.

-Objectives & Assessment
The overall course objective is to provide the student with a broad understanding of the main fundamentals of the structure of proteins. Each course section will have it's own individual objectives, which may be the subject of continuous self-assessment using forms provided by us.

-Course Map, or Contents Page (this page HTMLised?)
Important to avoid students from `wandering off' through any external hlinks that we offer, and to enable them to get back to where they want to be easily. Possibly using click buttons as in the O manual - see http://kaktus.kemi.aau.dk/oman/junk.html. VSNS-PPS STYLE GUIDE will soon appear.

OVERVIEW OF PROTEIN SYNTHESIS

-Cellular Organisation Mark Dalton is helping with this area
distinguish prokaryotes and eukaryotes, nucleus, DNA, chromosomes, membrane(s), cytosol, ER, lumen of ER, Golgi, organelles, ribosomes, mention viruses(?)

-Transcription
DNA, Watson-Crick A:T, G:C, unwinding of double helix, RNA polymerase, U not T, template directed synthesis of ssRNA ->rRNA, tRNA, mRNA, introns/exons in eukaryotes, splicing (regulation, operons and promoters?)

-Translation Garry Myers and Ted Crusberg offered help here
ribosome, attachment to Shine-Dalgarno sequence, genetic code, start (Met) and stop codons, coding sequence = gene, tRNA-AA, growth of nascent AA-chain and folding up, mention chaperones

-Post-translational processing
distinguish ER-directed vs. cytoplasmic, signal peptide Ted Crusberg?, peptidase, foldases, glycosylation, myristoylation, oligomerisation, binding of co-factors, etc

-Transport Ted Crusberg offered help here
into ER, to Golgi, lysosomes & export, to and across membrane, exocytosis, nuclear targeting, pores and channels, binding proteins, periplasm, circulatory systems in higher organisms

-Degradation Beatrice Gorinsky has contributed here

PRIMARY STRUCTURE OF PROTEINS

-Nomenclature (Genetic & Single-Letter Codes)Garry Myers has offered help here
Bases, reading frames, genetic code, 20 AAs, 3 and 1 letter codes, self-assessment form to test rote learning. Note sulphur in M, C.

-Databases - Phil Bourne at Columbia has elected to do this sub-section

Advances in sequencing, HUGO, automatic recognition and translation of coding ORFs, protein and DNA databases, NBRF-PIR, EMBL, GENBANK, SwissProt, Japan DB, GDB, non-redundant

-

PROTEIN GEOMETRY

Jon Cooper (Birkbeck) has agreed to look after this section - help welcome
-Nomenclature
Greek letters; N- & C-termini (chain direction); single-letter code. Different methods of representation (ball & stick, points & lines; space-filling; atomic radii. Colour conventions.

-The Peptide Bond
Condensation reaction. Planar bond; charge delocalisation; semi-rigidity. Bond lengths and angles. H-bonding potential.

-Torsion Angles 1.Main Chain phi/psi
Definition of torsion angle. Explanation of phi `before' and psi `after' C-alpha. Steric hindrance leads to preferred values. Refer forward to Rama plot & secondary structures Refer back to Glycine and Proline.

-Torsion Angles 2.Side Chain Rotamers
Steric hindrance leads to preferred values. gauche + and -, & trans, more populated in known structures. Packing in core.

-Ramachandran Plot
Who was he? What is the plot, and what does it show. Refer to secondary structures, and to turns (alpha-left). Maybe polyproline and bridge regions. Why is it useful?

OVERVIEW OF MOLECULAR FORCES

Oliver Smart has agreed to coordinate this section
-Covalent Bonds; Lengths and Angles (& distortions thereof)
Bond concept. Geometric data. Strong forces involved in bond stretching or breaking. Lesser in angle distortion. Functional form(?) and approx.values(?) Lennard-Jones (6-12). Aromatic rings(?)

-Van der Waals
Forces Radii; electron clouds. Non-bonded! Dipoles and induced dipoles. Lennard-Jones (6-12). Magnitudes.

-Hydrogen Bonds
Proton `sharing'. Donors and acceptors. Angle and distance limits. Importance to main-chain folds. Importance of H2O. Energy magnitudes.

-Electrostatic Effects, Salt Bridges
Coulomb attraction and repulsion. Screening effect of H2O and core atoms. Local fields, pKa changes. GRASP(?) Examples of salt bridges (mainly surface).

-The Hydrophobic Effect
Entropy of solvent (dG=dH-TdS), effects at surface, partition coeffts., `greasy' vs. hydrophilic (polar & charged). Magnitude of effect. Importance to folding (core vs.surface). Hydropathy plots and sliding window(?)

-The Importance of Solvent
Dry proteins denature! In folding and solubility, and in many reaction mechanisms.

-Overall Energetics, Stability, & Energy Minimisation
Add all terms together. Relate to folding (& pathway). Marginal stability. Thermophiles(?) Computational minimisation.

SECONDARY STRUCTURE

Kurt Berndt of the Karolinska Institute has elected to produce this section. He would probably welcome help :-)

-General, including representations, CD, prediction etc
Remind primary, secondary, super-secondary, tertiary, quaternary Folding produces strands and helices first. Such structures in most proteins - `architectural elements'. Arrows and cylinders. Strands lie together in sheets. Examples. (Cameo on circular dichroism?) Page on secondary structure prediction.

-The Alpha Helix 1.
The classic right-handed alpha-helix. Hydrogen bonding pattern 3.6 per turn. 100 degree turn. Carbonyls all pointing `down' - macrodipole. Few prolines and few glycines. Side chains sticking out. Graphical examples. Linus Pauling.

-The Alpha Helix 2.
Variations on the theme (3-10, pi). Amphipathicity. Capping(?). AA propensities. Length variation. Trans-membrane helices.

-Beta Sheets 1.Parallel
The concept of the extended strand in detail (inc.direction). H-bonding between adjacent strands. Pleated(ness). Silks.

-Beta Sheets 2.Anti-Parallel
Different H-bonding pattern. Also pleated. Hairpins.

-Beta Sheets - General
Twist. Mixed sheets. 1, +2x, etc nomenclature. Refer forward to folds

-Turns
Predominance of Pro & Gly. Positive phi. Tight turns; hairpins, classification(s). (P-loop in nucleotide-binders?)

-`Random' Coil
All the loops in between, which are not hairpins. Connecting sec.struct.elements. Often at surface. Evolutionary variability. Indels.

SUPER-SECONDARY STRUCTURE

Jon Cooper at Birkbeck will coordinate this section

-Motifs comprised of combinations of elements

-Beta hairpin

-Helix hairpin

-Helix-turn-helix (DNA binding vs EF-hand)

-beta-alpha-beta as in wound alpha-beta proteins and the right-handed crossover

-(?)beta corners

-and others(?) eg coiled-coil, poly-proline helix

TERTIARY STRUCTURE

- Membrane Proteins
Describe receptors, channels, pores and pumps in outline. Distinguish membrane associated, and integral membrane proteins.

-Fibrous and Structural
Cytoskeleton and Extra-Cellular Matrix. Describe collagen, keratin, and some other ECM proteins. Actin, etc.

-Globular (mainly enzyme)
Most biochemistry mediated by (1000s of) enzymes; mostly soluble and cytosolic. Cover co-factors. Also eg hormones. Plus all the cellular machinery. Then some plasma stuff(?). Page on exptl(?) X-Ray & NMR methods.

-Domains Distinct folding units. Give examples.
Sowdhamini and Stephen Ruffino will contribute here
Show difficulties of exact definition (compound domains). Use small disulphide domains as paradigm. Zinc fingers. Multi-domain structures.

-Mosaic Proteins
Mainly extra-cellular. Intron/exon boundaries. Exon-shuffling in evolution. Receptors and ECM proteins. Examples with diagrams (a la Campbell and Patthy)

PROTEIN FOLDS

General - classification and representation (point to SCOP?)
AA propensities different for classes, and for environments. Drawings, nomenclatures, etc.

All alpha ? point to some of Simon Brocklehurst's cytokines?
ROP, 4-helix bundle, globins, some cytokines Leucine zippers, Cyt-C peroxidase, citrate synthase Plenty of lovely graphical examples, please :-)

All beta
  1. anti-parallel - single sheets (subtilisin inhibitor) Ig sandwich, up-down barrels (retinol-binding prot etc) lectins, Greek keys, jelly rolls Plenty of lovely graphical examples.

  2. parallel - pectate lyase, alkaline protease, p22 tailspike protein. Plenty of lovely graphical examples.

Wound alpha/beta, and variations
mainly enzymes, mainly cytosolic. Rossman fold, and variations on theme. A huge section!? nucleotide-binding proteins. Tim barrels. Plenty of lovely graphical examples.

Mixed alpha+beta
Ribonuclease, lysozome, serpins, etc. Plenty of lovely graphical examples.

Other distinctive folds
eg beta propellor
eg alpha-beta horseshoe (RNase inhibitor)
eg beta-trefoil fold
eg . . .

QUATERNARY STRUCTURE

-Dimers, Trimers, Tetramers & +
Judith Murray-Rust has offered growth-factor dimers
Mainly in cytosolic enzymes, but also eg hormones, cytokines Haemoglobin. Receptor dimerisation. Symmetry/anti-symmetry Examples.

-Multi-enzyme complexes, Chaperonins, Cellular `Machinery'
tryptophan synthase(?), Reverse transcriptase polymerases, GroeL, - a mixed bag, help!

-Families and Superfamilies
see SCOP URL http://www.bio.cam.ac.uk/scop refer forward to next section of course

-Functional Groupings
EC enzyme classification. Hydrolases, transferases, isomerases, etc. Four major protease groupings. Cytokines, Kinases, etc

PROTEIN INTERACTIONS

-Enzymes, Catalysis, Active sites - Jon Cooper has offered protease active sites + inhibitors
Biochemical pathways, reactions, catalysts, substrate-> product active site clefts, mechanisms, triads, cofactors. Examples, eg acetylcholinesterase Joel Sussman, lysozyme, xylose isomerase, trypsin(?)

-Cooperativity, Allosteric Effects
Explanation of allostery and cooperativity in enzymes Haemoglobin, glycogen phosphorylase, and other examples

-Conformational Changes (related to function, regulation?)
Hinge motions. Serpins. F1 ATPase. Actin/myosin.

-Interactions among Proteins (receptors, carriers, Igs, hydrolases, etc)
Christine Slingsby may contribute here
Binding to receptors, their activation (dimerisation and activation). Proteolysis in processing and degradation. Carriers, eg transferrin, ferritin, retinol-b-pr., other means of transport.

Alan Mills.... 13th and  24th.October, 11th and 21st.November, 7th.December  1994
_______________________________________________________________________________
Tel: (01)71-631-6851 (Work)   FAX: (01)71-631-6803 (Work)         
       (01)71-223-7895 (Home)           (01)71-924-1266 (Home)         
  E-mail  :   a.mills@cryst.bbk.ac.uk
       or    ubcg05b@cryst.bbk.ac.uk
     URL   http://www.cryst.bbk.ac.uk/personal/a_mills.html
Snail-mail: Room 214, Crystallography Department,  
            Birkbeck College, University of London,
            Malet Street, LONDON  WC1E 7HX  Britain
_______________________________________________________________________________

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