Course Backbone (Alan Mills)

This is Alan's evolving draft for the course backbone. Later versions will probably be posted at Birkbeck.

Oct 25

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
........................................and subsequently  on 24th.October 1994
see also URLs


		as PMR has previously listed, plus any amendments.   We may
cite references for those who need a little revision.    Such stuff will be
sent to all 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 prevent 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


	 -Cellular Organisation 
		distinguish prokaryotes and eukaryotes, nucleus, DNA,
		chromosomes, membrane(s), cytosol, ER, lumen of ER, Golgi,
		organelles, ribosomes, mention viruses(?) 

		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?)

		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,
		peptidase, foldases, glycosylation, myristoylation,
		oligomerisation, binding of co-factors, etc

		into ER, to Golgi, lysosomes & export, to and across membrane,
		exocytosis, nuclear targeting, pores and channels, binding 
		proteins, periplasm, circulatory systems in higher organisms

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

                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

	-The Amino Acids & Their Properties 
                Re-emphasise single letter code (more sensitive alignment)

	 	0.Chemical Structure
			Diagrams, note hydrogens, acid + base, RASMOL samples, 
			peculiarity of Glycine and Proline, rote learning	
			smallest to largest, relationship to acceptance of
			mutations, influence on flexibility for Glycine
			D, E negative; H, K, R positive.   Effect of pH,
			i.e.pKa (esp. H). H-bonding & solvent.  Salt-bridges.
                        A, V, L, I, M definitely.  Simple meaning of term,
			Also F, P, W, C, Y, T, G, and R to some extent; each 
			needs discussing. 
                        F, Y, W - chemical stability of benzene ring, electron
			delocalisation, ring currents(?), interactions to pi 
			N, Q, S, T, also Y, W - hydrogen bonding donor/acceptor
                        interactions to solvent, and to m/c & s/c.
		6.Conformationally unusual
			G - flexible due to lack of steric hindrance
			P - inflexible due to s/c bonding back phi~-60 degrees
		Point up difference between L- and D- amino acids		
                and also that several carbon atoms within side chains are
                chiral.   Tetrahedral geometry

	-The Disulphide Bond
		Explain that nearby cysteines can be oxidised to form
		disulphides, which may improve stability.   Bridges are 
		common in extracellular proteins (and ER lumen) but rare in
		cytosolic proteins.  Converse is true for isolated thiols.
		Summarise geometry.   Refer to thiol-redox mechanisms &
		proteins.  ?canonical disulphide in Igs.  Cross-linking.

		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?


	-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.  & in many 
		reaction mechanisms.

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


	-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.  No 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
		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.


	-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(?)	


	-Globular (mainly enzyme) vs Fibrous, Structural, and Membrane Proteins
		Most biochemistry mediated by (1000s of) enzymes; mostly
		soluble and cytosolic.  Cover co-factors.  Also eg hormones. 
		Plus all the cellular machinery.   Describe collagen, keratin, 
		and some other ECM proteins.  Then some plasma stuff(?).   
		Distinguish membrane associated, and integral membrane
		proteins.  Describe receptors, channels, pores and pumps in
		outline.  Page on exptl(?) X-Ray & NMR methods.

                Distinct folding units.   Give examples.  Show difficulties of
		exact definition (compound domains).   Use small disulphide 
		domains as paradigm.  Zinc fingers.   Multi-domain structures.

        -Folds; classification and representation    (point to SCOP?)
			AA propensities different for classes, and for
			environments.  Drawings, nomenclatures, etc.
	        1.All alpha
			ROP, 4-helix bundle, globins, some cytokines
			Plenty of lovely graphical examples.
		2.All beta
			Ig sandwich, up-down barrels, lectins, Greek keys,
			jelly rolls
			Plenty of lovely graphical examples.
		3.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.
		4.Mixed alpha+beta
			Ribonuclease, lysozome, serpins, etc.		
			Plenty of lovely graphical examples. 
		5.Other distinctive folds
			eg beta propellor
			eg alpha-beta horseshoe (RNase inhibitor)
			eg beta-trefoil fold
			eg . . . 

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

	-Dimers, Trimers, Tetramers & +
		Mainly in cytosolic enzymes, but also eg hormones, cytokines
		Haemoglobin. Receptor dimerisation.   Examples.

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

	-Families and Superfamilies
		see SCOP URL
		refer forward to next section of course

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

	-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)
		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                         ........................  24th.October 1994

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Sept 30 1994