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)