Molecular Cell Biology

Animations of the Inner Life of the Cell.

These YouTube video's are really fascinating. 

"Nuclei, proteins and lipids move with bug-like authority, slithering, gliding and twisting through 3D space. All of those things that you see in the animation are going on in every one of your cells in your body all the time”

1: Wikipedia-TheInnerLifeOfTheCell  
2: multimedia.mcb.harvard.edu   
3: Inner Life of the Cell with commentary
4: Inner Life of the Cell and short version

5: Journey Inside the Cell

or see Video Bar gadget

Crystallization conference

ICCBM13-Dublin.

13th International Conference on the Crystallization of Biomolecular Macromolecules at Trinity College, Dublin, Ireland (September 2010). Motto: 'Enjoy, Learn, Network'. 
ICCBM13 focused on challenging systems to include macromolecular complexes and membrane proteins with an emphasis on novel practical as well as mechanistic aspects of crystallogenesis. 
The workshop was excellent for improving crystallization skills, in particular for membrane proteins. Did meet a lot of international colleagues during the workshop and the conference. The Irish pubs with live music performances were outstanding. I do admire the Irish for being so friendly (Céad Míle Fáilte).

Links: Conference website and pictures gallery.

campus - Trinity College

 

Trinity College

 Old Library - Trinity College

 Trinity College

 

Crystallization Workshop

in the Membrane Structural and Functional Biology Group laboratories at Trinity College Dublin

 

Crystallization conference 

 Irish Pub

 Temple Bar, most famous Irish Pub

 

 Mutefish (Mutefish website and YouTube)

 

 boulevard between Dublin and Dalkey

coastal town Dalkey

Structures

Selection of publications:

• Protein X-ray structures (with pdb accession codes)

PDB Structural Database

birefringent protein crystals

protein structures can be elucidated using X-ray diffraction data from protein crystals

recent structure:
GAPR-1 complex (4AIW)

GAPR-1n complex with lipid-binding inhibitor I6P

Schouten et al. Interaction of GAPR-1 with lipid bilayers is regulated by alternative homodimerization (2012) Biochimica et Biophysica Acta (BBA) - Biomembranes 1818: 2175–2183
 

Human complement factor B (2OK5)

Factor B

HEK293-S glycosylation

Milder et al. Factor B structure provides insights into activation of the central protease of the complement system (2007) Nat.Struct.Mol.Biol. 14: 224-228  

 

Complement component C2a (2I6Q and 2I6S)

C2a

Milder et al. Structure of complement component c2a: implications for convertase formation and substrate binding (2006) Structure 14: 1587-1597

Glutathione S-transferase (1M0U)

GST-2

Agianian et al. Structure of a Drosophila Sigma Class Glutathione S-transferase Reveals a Novel Active Site Topography Suited for Lipid Peroxidation Products (2003) J.Mol.Biol. 326: 151-16


Phosphatidylinositol transfer protein alpha (1KCM)

PITP-alpha

closed and open conformation of the PITP protein

Wirtz et al. Phosphatidylinositol transfer proteins: From closed for transport to open for exchange (2006) Advances in enzyme regulation, 46, 301-311.

crystallographic dimer

Van Tiel et al. The structure of phosphatidylinositol transfer protein alpha reveals sites for phospholipid binding and membrane association with major implications for its function (2002) FEBS letters, 531, 69-73.

Schouten et al. Structure of apo-phosphatidylinositol transfer protein alpha provides insight into membrane association (2002) EMBO J. 21: 2117-2121                                   

 play video above: switching between the open and closed structures of PITP

Leech-antiplatelet protein (1I8N)

rLAPP

Huizinga et al. The structure of leech anti-platelet protein, an inhibitor of haemostasis (2001) Acta Crystallogr.,Sect.D 57: 1071-1078

Beta2 glycoprotein I (1QUB)

B2GP-I

Bouma et al. Adhesion mechanism of human beta(2)-glycoprotein I to phospholipids based on its crystal structure (1999) EMBO J. 18: 5166-5174

• Other studies

L-amino acid methyl esters

 

X-ray structure of L-Serine methylester hydrochloride

 

Schouten et al. L-Serine methyl ester hydrochloride (2009) Acta Cryst. E65, o3026 (IUCr VM2012) 

 

Lutz et al. L-Alanine methyl ester hydrochloride monohydrate (2011) Acta Cryst. E67, o586 (IUCr EZ2229)

 

Study of microgravity crystal growth   

 

A new upside-down geometry is proposed to achieve the beneficial effects of microgravity crystal growth by making use of buoyant forces instead of compensating for them. 

Poodt et al. Simple geometry for diffusion limited protein crystal growth: harnessing gravity to suppress convection (2009) Crystal Growth & Design, 9, 885-888

Publications

Publication list.

CSC     : Publications 1996-2007 (Crystal and Structural Chemistry)

NARCIS: Publications 2002-2009 (National Academic Research and Collaborations Information System)

all publications 1983-2016 (see below)

[ 1.] Bouwstra, J.A., Schouten, A. & Kroon, J. (1983).

Acta Cryst. C39, 1121-1123.

Structural Studies of the System trans-Azobenzene/trans-Stilbene. 

I. A Reinvestigation of the Disorder in the Crystal Structure of trans-Azobenzene.

[ 2.] Klop, E.A., Schouten, A., van der Sluis, P. & Spek, A.L. (1984).

Acta Cryst. C40, 51-53.

Structure of Calcium Acetate Monohydrate.

[ 3.] Bouwstra, J.A., Schouten, A. & Kroon, J. (1984).

Acta Cryst. C40, 428-431.

Structural Studies of the System trans-Azobenzene/trans-Stilbene.

II. A Reinvestigation of the Disorder in the Crystal Structure of trans-Stilbene.

[ 4.] Bouwstra, J.A., Schouten, A., Kroon, J. & Helmholdt, R.B. (1985).

Acta Cryst. C41, 420-426.

Structural Studies of the System trans-Stilbene/trans-Azobenzene.

III. The Structures of Three Mixed Crystals of trans-Azobenzene/trans-Stilbene;

Determinations by X-ray and Neutron Diffraction.

[ 5.] Kanters, J.A., de Koster, A., Schouten, A., Venkatasubramanian, K. & Poonia, N.S. (1985).

Acta Cryst. C41, 1585-1588.

Structure of Bis(triethanolamine)bis(2,4,6-trinitrophenolato)barium(II).

[ 6.] Kanters, J.A., van der Steen, F.H., Schouten, A., Pushpa Bagdi & Poonia, N.S. (1986).

J. Incl. Phenom. 4, 225-233.

Synthesis and Crystal Structure of Ammonium (Picrate) (Dibenzo-18-crown-6).

[ 7.] van der Sluis, P., Schouten, A. & Spek, A.L. (1987).

Acta Cryst. C43, 1922-1924.

Structure of a Second Polymorph of Calcium Acetate Monohydrate.

[ 8.] Koole, L.H., Buck, H.M., Kanters, J.A. & Schouten, A. (1987).

Can. J. Chem. 65, 326-331.

Molecular conformation of 2'-deoxy-3',5'-di-O-acetyl adenosine.

Crystal structure and high resolution proton nuclear magnetic resonance investigations.

[ 9.] Koole, L.H., Buck, H.M., Kanters, J.A. & Schouten, A. (1988).

Can. J. Chem. 66, 2634-2639.

Molecular conformation of 2'-deoxy-3',5'-di-O-acetyl guanosine.

Crystal structure and high resolution proton nuclear magnetic resonance investigations.

[10.] Kuipers, W., Kanters, J.A. & Schouten, A. (1989).

Acta Cryst. C45, 482-485.

Structure of 1,4-Phenylenebis(3,3-diphenylketenimine).

[11.] van Vliet, P.M., Schouten, A., Kanters, J.A. & Buck, H.M. (1989).

Acta Cryst. C45, 1384-1387.

Structure of 3-[N-Methyl-N-(S)-a-methylbenzyl]-carbamoyl-1,2,4-trimethylpyridinium Iodide.

[12.] Kanters, J.A., Schouten, A., Kroon, J., Mathlouthi, M., van der Maas, J.H. & Lutz, B. (1989).

Acta Cryst. C45, 1934-1937.

Diheterolevulosan IV: Di-b-d-fructopyranose 1,2':2,1'-Dianhydride.

[13.] Schouten, A., Kanters, J.A. & Poonia, N.S. (1990).

Acta Cryst. C46, 61-64.

Structure of Caesium Picrate.

[14.] Kanters, J.A., Schouten, A., van der Sluis, P. & Duisenberg, A.J.M. (1990).

Acta Cryst. C46, 71-74.

Structure of d-Perseitol (d-glycero-d-galacto-Heptitol).

[15.] Aagaard, O.M., Janssen, R.A.J., de Waal, B.F.M., Kanters, J.A., Schouten, A. &

Buck, H.M. (1990).

J. Am. Chem. Soc. 112, 5432-5447. 

Intermolecular-Directed Reactivity in Solid Media. Radiogenic Formation of Phosphorus-Centered Radicals in Chiral Diphosphine Disulfides Studied by ESR.

[16.] Baran, J., Kanters, J.A., Lutz, E.T.G., van der Maas, J.H., Schouten, A. &

Wierzejewska-Hnat, M. (1990).

J. Mol. Struct. 222, 305-317.

Polarized FTIR spectra and low temperature structure of adamantanol derivatives.

Part I. 2-(2,4,6-Trimethylphenyl)adamantan-2-ol.

[17.] Kanters, J.A., Schouten, A. & van Bommel, M. (1990).

J. Mol. Struct. 238, 403-412.

Crystal and molecular structure of the dihydrate of the artificial sweetener Lactitol:

4-O-b-d-galactopyranosyl-d-glucitol.2H₂O.

[18.] van der Sluis, P., Schouten, A. & Kanters, J.A. (1990).

Acta Cryst. C46, 2165-2168.

Structure of Chenodeoxycholic Acid in Chenodeoxycholic Acid Ethyl Acetate Solvate.

[19.] Kanters, J.A., Schouten, A. & van Bommel, M. (1990).

Acta Cryst. C46, 2408-2411.

Structure of Lactitol (4-O-b-d-Galactopyranosyl-d-glucitol) Monohydrate: an Artificial Sweetner.

[20.] Schouten, A. & Kanters, J.A. (1990).

Acta Cryst. C46, 2484-2486.

Structure of a Glycouril Derivative: Tetrahydro-1,6:3,4-di(methanoxymethano)-3a,6a-dimethylimidazo[4,5-d]imidazole-2,5(1H,3H)-dione.

[21.] Kanters, J.A, Schouten, A., Kroon, J. & Grech, E. (1991).

Acta Cryst. C47, 807-810.

Structure of 8-Dimethylamino-1-dimethylammonionaphthalene Hydrogen Squarate.

[22.] Schouten, A. & Kanters, J.A. (1991).

Acta Cryst. C47, 1320-1322.

Structure of the Hexagonal Modification of 3'-O-Acetylthymidine.

[23.] Schouten, A. & Kanters, J.A. (1991).

Acta Cryst. C47, 1754-1756.

Structure of the Triclinic Modification of

17b-Hydroxy-19-nor-7a-methyl-17a-pregn-5(10)-en-20-yn-3-one (ORG OD14).

[24.] Kanters, J.A., Schouten, A., Duisenberg, A.J.M., Glowiak, T., Malarski, Z., Sobczyk, L. & Grech, E. (1991).

Acta Cryst. C47, 2148-2151.

Temperature Effect on the Structure of the Complex

1,8-Bis(dimethylamino)naphthalene-Chloranilic Acid (2/1) Dihydrate.

[25.] Kanters, J.A., Kroon, J., Hooft, R., Schouten, A., van Schijndel, J.A.M. &

Brandsen, J. (1991).

Croatica Chemica Acta 64, 353-370.

Temperature-Dependent Order-Disorder Phenomena in Crystal Structures Containing Dimers of Carboxylic Acids:

The Crystal and Molecular Structure of 3,5-Dinitrobenzoic Acid at Room and Liquid Nitrogen Temperature and Statistics of the Geometries of Hydrogen-Bonded Carboxyl Groups.

[26.] Kanters, J.A., Schouten, A., Steinwender, E., van der Maas, J.H., Groenen, L.C.

& Reinhoudt, D.N. (1992).

J. Mol. Struct. 269, 49-64.

Spectroscopic and crystallographic study of 27,28-diethoxy-p-tert-butylcalix[4]arenes.

[27.] Kanters, J.A., Schouten, A., Kroon, J. & Grech, E. (1992).

Acta Cryst. C48, 1254-1257.

Complexes of the `Proton Sponge' 1,8-Bis(dimethylamino)naphthalene (DMAN).

IV. Structure of [DMANH]₂⁺.[Squarate]^2– Tetrahydrate at 100 K.

[28.] Schouten, A. & Kanters, J.A. (1993).

Acta Cryst. C49, 1376-1378.

Structure of the Benzo-15-crown-5-3,5-Dinitrobenzoic Acid-Water (1/1/1) Complex.

[29.] Kanters, J.A., Schouten, A., Sterk, G.J. & de Jong, M.H. (1993).

J. Mol. Struct. 298, 113-120.

Crystallographic study of three coronary vasolidators of the nitrate ester type:

1,4-trans-cyclohexanedimethanol dinitrate,

1,4:3,6-dianhydro-d-glucitol-2,5-dinitrate and

1,4:3,6-dianhydro-d-glucitol-2-mononitrate. 

[30.] Keegstra, E.M.D., Schouten, P.G., Schouten, A., Kooijman, H., Spek, A.L., de Haas, M.P., Zwikker, J.W., Warman, J.M. & Jenneskens, L.W. (1993).

Recl. Trav. Chim. Pays-Bas 112, 423-424.

Rapid Charge Migration within 1,4-Benzoquinone Stacks in the Solid Phases of

2,5-Di-n-decoxy-1,4-benzoquinone.

[31.] Broeders, N.L.H.L., van der Heiden, A.P., Koole, L.H., Kanters, J.A. & Schouten, A. (1993).

Can. J. Chem. 71, 855-863.

2'-O-Methyl-cis-adenosine 3',5'-cyclic methyl monophosphate, a new model system for cAMP. Aspects of structure and reactivity.

[32.] Schouten, A., Kanters, J.A. & Kroon, J. (1994).

Acta Cryst. C50, 128-129.

Structure of Org 32763: 3-Methoxyimino-quinuclidinium Chloride.

[33.] Schouten, A., Kanters, J.A. & van Krieken, J. (1994).

J. Mol. Struct. 323, 165-168.

Low temperature crystal structure and molecular conformation of l-(+)-lactic acid.

[34.] Moree, W.J., Schouten, A., Kroon, J. & Liskamp, R.M.J. (1995).

Int. J. Peptide Res. 45, 501-507.

Peptides containing the sulfonamide transition-state isostere:

synthesis and structure of N-acetyl-tauryl-l-proline methylamide.

[35.] Keegstra, E.M.D., Huisman, B.H., Paardekooper, E.M., Hoogesteger, F.J., Zwikker, J.W., Jenneskens, L.W., Kooijman, H., Schouten, A., Veldman, N. & Spek, A.L. (1996).

J. Chem. Soc. Perkin Trans. 2, 229-240.

2,3,5,6-Tetraalkoxy-1,4-benzoquinones and structurally related tetraalkoxy benzene derivatives: synthesis, properties and solid state packing motifs.

[36.] Keegstra, E.M.D., van der Mieden, V., Zwikker, J.W., Jenneskens, L.W., Schouten, A., Kooijman, H., Veldman, N. & Spek, A.L. (1996).

Chem. Mater. 8, 1092-1105.

Self-Organization of 2,5-Di-n-Alkoxy-1,4-benzoquinones in the Solid State:

Molecular Recognition Involving Intermolecular Dipole-Dipole, Weak C--H...O=C Hydrogen Bond and van der Waals Interactions.

[37.] Sliedregt, K.M., Schouten, A., Kroon, J. & Liskamp, R.M.J. (1996).

Tetrahedron Letters 37, 4237-4240.

Reaction of N-Trityl amino acids with BOP:

Efficient synthesis of t-Butyl esters as well as N-Trityl Serine- and Threonine-b-lactones.

[38.] Schouten, A., Kanters, J.A., Kroon, J., Comini, S., Looten, P. & Mathlouthi, M. (1998).

Carbohydrate Research 312, 131-137.

Conformational polymorphism of d-sorbitol (d-glucitol):

the crystal and molecular structures of d-glucitol 2/3-hydrate and epsilon d-glucitol.

[39.] Lutz, B., van der Maas, J.H., Schouten, A. & Kanters, J. (1998).

Association Andrew van Hook  47-53.

Variable low temperature FT-IR.

A method to discriminate non H-bonded and H-bonded hydroxyl groups in carbohydrates.

L’ Infrarouge moyen dans l’analyse des sucres, comptes rendus, 5^e symposium international, Reims, 18 mars 1998.

[40.] Ravelli, R.B.G., Raves, M.L., Scheres, S.W.H., Schouten, A. & Kroon, J. (1999).

J. Synchrotron Rad. 6, 19-28.

Ab initio structure determination of low-molecular-weight compounds using synchrotron radiation Laue diffraction.

[41.] [1QUB]

Bouma, B., de Groot, P.G., van den Elsen, J.M.H., Ravelli, R.B.G., Schouten,A., Simmelink, M.A.J., Derksen, R.H.W.M., Kroon, J. & Gros, P. (1999).

The EMBO Journal 18, No.19, 5166-5174. 

Adhesion mechanism of human b₂-glycoprotein I to phospholipids based on its crystal structure.

[42.] Schouten, A., Kanters, J.A., Kroon, J., Looten, P., Duflot, P. & Mathlouthi, M. (1999).

Carbohydrate Research 322, 274-278.

Crystal and molecular structure of maltotriitol (4-O-a-d-glucopyranosyl-4-O-a-d-

glucopyranosyl-d-glucitol).

[43.] Schouten, A., Kanters, J.A., Kroon, J., Looten, P., Duflot, P. & Mathlouthi, M. (1999).

Carbohydrate Research 322, 298-302.

A redetermination of the crystal and molecular structure of maltitol (4-O-a-d-glucopyranosyl-d-glucitol).

[44.] [1I8N]

Huizinga, E.G., Schouten, A., Connolly, T.M., Kroon, J., Sixma, J.J. & Gros, P. (2001).

Acta Cryst. D57, 1071-1078. 

The structure of leech-antiplatelet protein, an inhibitor of haemostasis.

[45.] [1KCM]

Schouten, A., Agianian, B.A., Westerman, J., Kroon, J., Wirtz, K.W.A. & Gros, P. (2002).

The EMBO Journal 21, No. 9, 2117-2121.

Structure of apo-phosphatidylinositol transfer protein a provides insight into membrane association.

[46.] van Tiel, C.M., Schouten, A., Snoek, G.T., Gros, P. & Wirtz, K.W.A. (2002).

FEBS Letters 531, 69-73.

Minireview: The structure of phosphatidylinositol transfer protein a reveals sites for phospholipid binding and membrane association with major implications for its function.

[47.] [1M0U]

Agianian, B., Tucker, P.A., Schouten, A., Leonard, K., Bullard, B. & Gros, P. (2003).

J. Mol. Biol. 326, 151-165.

Structure of a Drosophila Sigma Class Glutathione S-transferase Reveals a Novel Active Site Topography Suited for Lipid Peroxidation Products.

[48.] K.M. Valentijn, R. de Koning, Y. Derks, J.M. Van Doorn, T.P. Van der Krift, A. Schouten, H.K. Koerten, D.J. Van der Horst, P. Gros, A.J. Koster, C.W. Rodenburg (2004).

Proceedings 13^th European Microscopy Congress Vol. III. Life Sciences, pp 327-328.

Preliminary three-dimensional model of insect lipoprotein HDLp by combining electron microscopy and X-ray crystallography;

University of Antwerp, Belgium

[49.] K.M. Valentijn, R. de Koning, Y. Derks, J.M. Van Doorn, T.P. Van der Krift, A. Schouten, H.K. Koerten, D.J. Van der Horst, P. Gros, A.J. Koster, C.W. Rodenburg (2004).

Microscopy and Microanalysis, pp 11514-11515.

Preliminary three-dimensional model of insect lipoprotein HDLp by using electron microscopy and X-ray crystallography;

MSA-EMC, Savanna, Georgia, USA

[50.] K.W.A. Wirtz, A. Schouten, P. Gros (2006).

Advan. Enzyme Regul. 46, 301-311.

Phosphatidylinositol transfer proteins: From closed for transport to open for exchange.

[51.] [2I6Q&2I6S: C2a (Mn, Li)]

Milder, F.J.,  Raaijmakers, H.C.,  Vandeputte, M.D.A.A.,  Schouten, A.,  Huizinga, E.G.,  Romijn, R.A.,  Hemrika, W.,  Roos, A.,  Daha, M.R.,  Gros, P. (2006).

Structure 14, 1587-1597.

Structure of complement component C2a: implications for convertase formation and substrate binding.

[52.] [2OK5]

Milder, Fin J., L. Gomes, A. Schouten, B.J.C. Janssen, E.G. Huizinga, R.A. Romijn, W. Hemrika, A. Roos, M.R. Daha, and P. Gros (2007).
Nature Structural & Molecular Biology 14, 224-228.

Factor B structure provides insights into activation of the central protease of the complement system.

[53.]

P. W. G. Poodt, M. C. R. Heijna, A. Schouten, P. Gros, W. J. P. van Enckevort, and E. Vlieg (2009).

Crystal Growth & Design  9, No. 2, 885.

Simple Geometry for Diffusion Limited Protein Crystal Growth: Harnessing Gravity to Suppress Convection.

[54.] [IUCr VM2012]

Arie Schouten, and Martin Lutz (2009).

Acta Cryst. E65, o3026.

l-Serine methyl ester hydrochloride.

[55.] [IUCr EZ2229]

Martin Lutz, and Arie Schouten (2011).

Acta Cryst. E67, o586.

l-Alanine methyl ester hydrochloride monohydrate.

[56.] [4AIW]

Josse van Galen, Nick K. Olrichs, Arie Schouten, Ramon L. Serrano, Esther N.M. Nolte-'t Hoen, Ruud Eerland, Dora Kaloyanova, Piet Gros, and J. Bernd Helms (2012).

Biochimica et Biophysica Acta (BBA) - Biomembranes 1818, No. 9, 2175–2183

Interaction of GAPR-1 with lipid bilayers is regulated by alternative homodimerization.

[57.]
E.F. Halff, C.A. Diebolder, M. Versteeg, A. Schouten, T.H. Brondijk, and E.G. Huizinga (2012).
J.Biol Chem (JBC) 287, No. 46, 38460
Formation and Structure of a NAIP5-NLRC4 Inflammasome Induced by Direct Interactions with Conserved N- and C-terminal Regions of Flagellin.

[58.]
Karine M Valentijn, Roman Koning, Yvonne Derks, Jan M Van Doorn, Theo P Van der Krift, Arie Schouten, Henk K Koerten, Dick J Van der Horst, Piet Gros, Abraham J Koster and Kees W Rodenburg (2004)
Microscopy and Microanalysis, Volume 10, Supplement S02, August 2004, pp 1514-1515

Preliminary Three-Dimensional Model of Insect Lipoprotein HDLp by Using Electron Microscopy and X-ray Crystallography.   

[59.] [5CM8, 5CM9]
Milica Popovic, Arie Schouten, Marije Rensen-de Leeuw, Holger Rehmann (2016).
J. Struct. Biol 193, 106
The structure of the Guanine Nucleotide Exchange Factor RLf in complex with the small G-protein Ral identifies conformational intermediates of the exchange reaction and the basis for selectivity.