Reuter Group | Publications

Publications 2016

Khan HM, Grauffel C, Broer R, MacKerell AD, Havenith RW, Reuter N (2016)
Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4(+) Interactions
J Chem Theory Comput, 12 (11), 5585-5595
PubMed 27682345

Khan HM, He T, Fuglebakk EGrauffel C, Yang B, Roberts MF, Gershenson A, Reuter N (2016)
A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding
Biophys J, 110 (6), 1367-78
PubMed 27028646

Martin KR, Kantari-Mimoun C, Yin M, Pederzoli-Ribeil M, Angelot-Delettre F, Ceroi A, Grauffel C, Benhamou M, Reuter N, Saas P, Frachet P, Boulanger CM, Witko-Sarsat V (2016)
Proteinase 3 Is a Phosphatidylserine-binding Protein That Affects the Production and Function of Microvesicles
J Biol Chem, 291 (20), 10476-89
PubMed 26961880

Tiwari SPReuter N (2016)
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
PLoS Comput Biol, 12 (3), e1004834
PubMed 27015412

Tiwari SPReuter N (2016)
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes
PLoS One, 11 (3), e1004834

Publications 2015

Chon NL, Osterberg JR, Henderson J, Khan HMReuter N, Knight JD, Lin H (2015)
Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions
Biochemistry, 54 (37), 5696-711
PubMed 26333120

Publications 2014

Budnjo A, Narawane S, Grauffel C, Schillinger AS, Fossen T, Reuter N, Haug BE (2014)
Reversible ketomethylene-based inhibitors of human neutrophil proteinase 3
J Med Chem, 57 (22), 9396-408
PubMed 25365140

Fuglebakk ETiwari SPReuter N (2014)
Comparing the intrinsic dynamics of multiple protein structures using elastic network models
Biochim Biophys Acta, 1850 (5), 911-22
PubMed 25267310

Grauffel C, Stote RH, Dejaegere A (2014)
Molecular dynamics for computational proteomics of methylated histone H3
Biochim Biophys Acta, 1850 (5), 1026-40
PubMed 25240462

Myklebust LM, Van Damme P, Støve SI, Dörfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T(2014)
Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects
Hum Mol Genet, 24 (7), 1956-76
PubMed 25489052

Narawane S, Budnjo A, Grauffel C, Haug BE, Reuter N (2014)
In silico design, synthesis, and assays of specific substrates for proteinase 3: influence of fluorogenic and charged groups
J Med Chem, 57 (3), 1111-5
PubMed 24397704

Perica T, Kondo Y, Tiwari SP, McLaughlin SH, Kemplen KR, Zhang X, Steward A, Reuter N, Clarke J, Teichmann SA (2014)
Evolution of oligomeric state through allosteric pathways that mimic ligand binding
Science, 346 (6216), 1254346
PubMed 25525255

Schillinger AS, Grauffel CKhan HM, Halskau O, Reuter N (2014)
Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter
Biochim Biophys Acta, 1838 (12), 3191-202
PubMed 25218402

Taxt AM, Diaz Y, Bacle A, Grauffel C, Reuter N, Aasland R, Sommerfelt H, Puntervoll P (2014)
Characterization of immunological cross-reactivity between enterotoxigenic Escherichia coli heat-stable toxin and human guanylin and uroguanylin
Infect Immun, 82 (7), 2913-22
PubMed 24778111

Tiwari SPFuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N (2014)
WEBnm@ v2.0: Web server and services for comparing protein flexibility
BMC Bioinformatics, 15, 427
PubMed 25547242

Yang B, Pu M, Khan HM, Friedman L, Reuter N, Roberts MF, Gershenson A (2014)
Quantifying transient interactions between Bacillus phosphatidylinositol-specific phospholipase-C and phosphatidylcholine-rich vesicles
J Am Chem Soc, 137 (1), 14-7
PubMed 25517221

Publications 2013

Cheng J, Karri S, Grauffel C, Wang F, Reuter N, Roberts MF, Wintrode PL, Gershenson A (2013)
Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding?
Biophys J, 104 (1), 185-95
PubMed 23332071

Fuglebakk EReuter N, Hinsen K (2013)
Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions
J Chem Theory Comput, 9 (12), 5618-28
PubMed 26592296

Grauffel C, Yang B, He T, Roberts MF, Gershenson A, Reuter N (2013)
Cation-π interactions as lipid-specific anchors for phosphatidylinositol-specific phospholipase C
J Am Chem Soc, 135 (15), 5740-50
PubMed 23506313

Parulek J, Turkay C, Reuter N, Viola I (2013)
Visual cavity analysis in molecular simulations
BMC Bioinformatics, 14 Suppl 19, S4
PubMed 24564409

Publications 2012

Bouayad D, Pederzoli-Ribeil M, Mocek J, Candalh C, Arlet JB, Hermine O, Reuter N, Davezac N, Witko-Sarsat V (2012)
Nuclear-to-cytoplasmic relocalization of the proliferating cell nuclear antigen (PCNA) during differentiation involves a chromosome region maintenance 1 (CRM1)-dependent export and is a prerequisite for PCNA antiapoptotic activity in mature neutrophils
J Biol Chem, 287 (40), 33812-25
PubMed 22846997

Fuglebakk E, Echave J, Reuter N (2012)
Measuring and comparing structural fluctuation patterns in large protein datasets
Bioinformatics, 28 (19), 2431-40
PubMed 22796957

Grauffel C, Abboud A, Liszczak G, Marmorstein R, Arnesen T, Reuter N (2012)
Specificity and versatility of substrate binding sites in four catalytic domains of human N-terminal acetyltransferases
PLoS One, 7 (12), e52642
PubMed 23285125

Romanowska J, Reuter N, Trylska J (2012)
Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes
Proteins, 81 (1), 63-80
PubMed 22907688

Skjaerven L, Muga A, Reuter N, Martinez A (2012)
A dynamic model of long-range conformational adaptations triggered by nucleotide binding in GroEL-GroES
Proteins, 80 (10), 2333-46
PubMed 22576372

Waheed Q, Tjörnhammar R, Edholm O (2012)
Phase transitions in coarse-grained lipid bilayers containing cholesterol by molecular dynamics simulations
Biophys J, 103 (10), 2125-33
PubMed 23200046

Publications 2011

Kantari C, Millet A, Gabillet J, Hajjar E, Broemstrup T, Pluta P, Reuter N, Witko-Sarsat V (2011)
Molecular analysis of the membrane insertion domain of proteinase 3, the Wegener’s autoantigen, in RBL cells: implication for its pathogenic activity
J Leukoc Biol, 90 (5), 941-50
PubMed 21821719

Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, Reuter N, Martinez A (2011)
Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations
PLoS Comput Biol, 7 (3), e1002004
PubMed 21423709

Skjaerven L, Martinez A, Reuter N (2011)
Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit
Proteins, 79 (1), 232-43
PubMed 21058295

Skjaerven L, Reuter N, Martinez A (2011)
Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach
Future Med Chem, 3 (16), 2079-100
PubMed 22098354

Waheed Q, Edholm O (2011)
Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice
J Chem Theory Comput, 7 (9), 2903-9
PubMed 26605479

Publications 2010

Broemstrup T, Reuter N (2010)
How does proteinase 3 interact with lipid bilayers?
Phys Chem Chem Phys, 12 (27), 7487-96
PubMed 20532386

Broemstrup T, Reuter N (2010)
Molecular dynamics simulations of mixed acidic/zwitterionic phospholipid bilayers
Biophys J, 99 (3), 825-33
PubMed 20682260

Hajjar E, Broemstrup T, Kantari C, Witko-Sarsat V, Reuter N (2010)
Structures of human proteinase 3 and neutrophil elastase–so similar yet so different
FEBS J, 277 (10), 2238-54
PubMed 20423453

Witko-Sarsat V, Mocek J, Bouayad D, Tamassia N, Ribeil JA, Candalh C, Davezac N, Reuter N, Mouthon L, Hermine O, Pederzoli-Ribeil M, Cassatella MA (2010)
Proliferating cell nuclear antigen acts as a cytoplasmic platform controlling human neutrophil survival
J Exp Med, 207 (12), 2631-45
PubMed 20975039

Witko-Sarsat V, Reuter N, Mouthon L (2010)
Interaction of proteinase 3 with its associated partners: implications in the pathogenesis of Wegener’s granulomatosis
Curr Opin Rheumatol, 22 (1), 1-7
PubMed 19881350

Publications 2009

Hajjar E, Dejaegere A, Reuter N (2009)
Challenges in pKa predictions for proteins: the case of Asp213 in human proteinase 3
J Phys Chem A, 113 (43), 11783-92
PubMed 19780520

Skjaerven L, Hollup SM, Reuter N (2009)
Normal mode analysis for proteins
Theochem-J. Mol. Struct., 898 (1-3), 42-48

Waheed Q, Edholm O (2009)
Undulation contributions to the area compressibility in lipid bilayer simulations
Biophys J, 97 (10), 2754-60
PubMed 19917229

Publications 2008

Hajjar E, Mihajlovic M, Witko-Sarsat V, Lazaridis T, Reuter N (2008)
Computational prediction of the binding site of proteinase 3 to the plasma membrane
Proteins, 71 (4), 1655-69
PubMed 18076025

Publications 2007

Daae Lampe O, Viola I, Reuter N, Hauser H (2007)
Two-level approach to efficient visualization of protein dynamics
IEEE Trans Vis Comput Graph, 13 (6), 1616-23
PubMed 17968117

Hajjar E, Korkmaz B, Reuter N (2007)
Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase
FEBS Lett, 581 (29), 5685-90
PubMed 18023421

Lampe OD, Viola I, Reuter N, Hauser H (2007)
Two-level approach to efficient visualization of protein dynamics
IEEE Trans. Vis. Comput. Graph., 13 (6), 1616-1623

Skjaerven L, Jonassen I, Reuter N (2007)
TMM@: a web application for the analysis of transmembrane helix mobility
BMC Bioinformatics, 8, 232
PubMed 17601351

Publications 2006

Brillard-Bourdet M, Hamdaoui A, Hajjar E, Boudier C, Reuter N, Ehret-Sabatier L, Bieth JG, Gauthier F (2006)
A novel locust (Schistocerca gregaria) serine protease inhibitor with a high affinity for neutrophil elastase
Biochem J, 400 (3), 467-76
PubMed 16839309

Hajjar E, Korkmaz B, Gauthier F, Brandsdal BO, Witko-Sarsat V, Reuter N (2006)
Inspection of the binding sites of proteinase3 for the design of a highly specific substrate
J Med Chem, 49 (4), 1248-60
PubMed 16480262

Korkmaz B, Hajjar E, Kalupov T, Reuter N, Brillard-Bourdet M, Moreau T, Juliano L, Gauthier F (2006)
Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase. A kinetic and molecular modeling analysis
J Biol Chem, 282 (3), 1989-97
PubMed 17088257

Rastogi S, Reuter N, Liberles DA (2006)
Evaluation of models for the evolution of protein sequences and functions under structural constraint
Biophys Chem, 124 (2), 134-44
PubMed 16837122

Publications 2005

Dublet B, Ruello A, Pederzoli M, Hajjar E, Courbebaisse M, Canteloup S, Reuter N, Witko-Sarsat V (2005)
Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line. Molecular analysis of the cleavage site
J Biol Chem, 280 (34), 30242-53
PubMed 15975933

Hollup SM, Salensminde G, Reuter N (2005)
WEBnm@: a web application for normal mode analyses of proteins
BMC Bioinformatics, 6, 52
PubMed 15762993

Publications 2004

Hinsen K, Reuter N, Navaza J, Stokes DL, Lacapère JJ (2004)
Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase
Biophys J, 88 (2), 818-27
PubMed 15542555

Publications 2003

Agasøster AV, Halskau Ø, Fuglebakk E, Frøystein NA, Muga A, Holmsen H, Martínez A (2003)
The interaction of peripheral proteins and membranes studied with alpha-lactalbumin and phospholipid bilayers of various compositions
J Biol Chem, 278 (24), 21790-7
PubMed 12660251

Reuter N, Hinsen K, Lacapère JJ (2003)
Transconformations of the SERCA1 Ca-ATPase: a normal mode study
Biophys J, 85 (4), 2186-97
PubMed 14507684

Publications 2002

Iversen H, Fuglebakk E, Holmsen H, Fukami MH (2002)
Identification of minor metabolites of phospholipid signal molecules in [(32)P]P(i)-labelled platelets
Platelets, 13 (5-6), 279-84
PubMed 12189013

Schöneboom JC, Lin H, Reuter N, Thiel W, Cohen S, Ogliaro F, Shaik S (2002)
The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations
J Am Chem Soc, 124 (27), 8142-51
PubMed 12095360