Physical Bioinformatics - A Case Study
Sequence and structure information are the bedrock on which anunderstanding of cellular functions and the underlying physical mechanismscan be built. This lecture illustrates how the two sources of information arecombined to investigate by means of the program VMD function andmechanism of the aquaporin family of membrane channels that transport waterand certain small solutes across cell walls. Introducing first the keyarchitectural features of a single aquaporin, structures and sequences of fouraquaporins are aligned and common features recognized. The shared anddistinct features are examined closely and used as guideposts leading quicklyto key questions regarding the mechanism underlying aquaporin's efficientconduction and selection. The questions are addressed by means of moleculardynamics simulations using the program NAMD that reveal the physicalprinciples behind water transport and highly selective solute co-transport inaquaporins. Sequence-structure information is viewed again to elucidatetetramer binding and pathologies connected with certain aquaporin mutants.The lecture introduces the concepts behind the programs employed andemphasizes those aspects of the case study that can be applied forinvestigations of other protein families.
Physical Bioinformatics - A Case StudyAquaporin Family of Membrane Channels
Klaus Schulten, U. Illinois at Urbana-Champaign
The Aquaporin Superfamily
Watertransport
Glyceroltransport
Heymann and Engel News Physiol. Sci. 14, 187 (1999)
(Animal)
(Animal)
(Bacterial)
(Bacterial)
(Bacterial)
(Bacterial)
(Bacterial)
(Plant)
(Yeast)
(Yeast)
(Yeast)
(Plant)
(Plant)
(Animal)
Water and Glycerol Channelsin the Human Body
lenstears
brain
salivary glands
lung
kidney
red blood cellsAquaporin-10
Fluid balance of the lensEye: lens fiber cellsAquaporin-0
LeukocytesAquaporin-9
Testis, pancreas, liverAquaporin-8
Testis and spermAquaporin-7
Very low waterpermeability!
KidneyAquaporin-6
Production of salivaProduction of tears
Salivary glandsLacrimal glands
Aquaporin-5
Reabsorption of waterCSF fluid balanceOsmosensing function?Bronchial fluid secretion
Kidney: collecting ductsBrain: ependymal cellsBrain: hypothalamusLung: bronchial epithelium
Aquaporin-4
Reabsorption of waterSecretion of water
Kidney: collecting ductsTrachea: epithelial cells
Aquaporin-3
ADH hormone activityKidney: collecting ductsAquaporin-2
Osmotic protectionConcentration of urineAqueous humorProduction of CSFAlveolar hydration
Red blood cellsKidney: proximal tubulesEye: ciliary epitheliumBrain: choriod plexusLung: alveolar epithelialcells
Aquaporin-1
Additional members are suspected to exist.
• Water and glycerol transport
• Exclusion of ions and protons
• Tetrameric arrangement in membrane
Functionally Important Featuresof Aquaporins
~100% conserved -NPA- signature sequence
NPA NPARN C
Aquaporins of known structure:Aquaporins of known structure:GlpF – E. coli glycerol channel (aquaglyceroporin)– Fu, et al., Science (2000)AQP1 – Mammalian aquaporin-1 (pure waterchannel) -Sui et al, Nature (2001)
E E
Load Aquaporin 1J4N into VMD
VMD Permits Different Rendering Styles
movietube
cartoon tube - transparent
Comparing Sequences of Aquaporins
Highlighting Key Conserved Residues
Load Aquaporins 1j4n, 1fqy, 1lda, 1rc2 into VMD
Aligning Structures and Sequences
Comparing Structures by Similarity - Q Value
Comparing Structures by Similarity - Q Value
Exhibiting Sequence Identity - Side View
Exhibiting Sequence Identity - Top View
Showing Conserved Residues - Monomer
Showing Conserved Residues - Tetramer
Dynamics of Protein, Lipid, Water System
M. Jensen, E. Tajkhorshid, K. Schulten, Structure 9, 1083 (2001)
note the curved adjustment between lipids-protein
Morten Jensen, Emad Tajkhorshid
Equilibrated Structure after 1 ns
Glycerol Conduction• Spontaneous glycerol conduction
on ns time scale;• Conduction occurs independently
in each monomer;• Exposed backbone carbonyl
oxygen atoms dictates glycerol andwater pathway; this explains thenon-helical secondary structure inthe aquaporin family;
• Glycerol resides at the positions ofconserved motif for the longesttime during simulation = minimumenergy sites;
• Water molecules are essential forthe glycerol transport.
M. Jensen, E. Tajkhorshid, K. Schulten, Structure 9, 1083 (2001)