Refereed Papers Book Chapters & Proceedings
 Refereed Papers
Pathways of Amyloid-β Aggregation Depend on Oligomer Shape
B. Barz, Q. Liao, B. Strodel
J. Am. Chem. Soc., 140: 319-327 (2018) [link]

Learning From Simulations.
B. Strodel
Pan European Networks: Health, 02: 91-92 (2017) [PDF]

Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions
Q. Liao, A. Pabis, B. Strodel, S.C.L. Kamerlin
J. Phys. Chem. Lett., 8: 5408-5414 (2017) [link]

Molecular Dynamics Simulations Reveal Key Roles of the Interleukin-6 Alpha Receptor in the Assembly of the Human Interleukin-6 Receptor Complex
O. Schillinger, V. Panwalkar, B. Strodel, A. Dingley
J. Phys. Chem. B, 121: 8113-8122 (2017) [link]

Shuffling Active Site Sub-State Populations Impacts Catalytic Activity: The Case of Glucose Oxidase
D. Petrovic, D. Frank, S.C.L. Kamerlin, K. Hoffmann, & B. Strodel
ACS Catal., 7: 6188-6197 (2017) [link]

Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase
Y. Kulkarni, Q. Liao, D. Petrovic, D.M. Krüger, B. Strodel, T.L. Amyes, J. Richard, S.C.L. Kamerlin
J. Am. Chem. Soc., 139: 10514-10525 (2017) [link]

Aβ42 pentamers/hexamers are the smallest detectable oligomers in solution
M. Wolff, B. Zhang-Haagen, C. Decker, B. Barz, M. Schneider, R. Biehl, A. Radulescu, B. Strodel, D. Willbold, & L. Nagel-Steger
Sci. Rep., 7: 2493 (2017) [link]

Protein Stability and Unfolding Following Glycine Radical Formation/strong>
M.C. Owen, I.G. Csizmadia, B. Viskolcz, & B. Strodel
Molecules, 22: 655 (2017) [link]

A combination of mutational and computational scanning guides the design of an artificial ligand-binding controlled lipase
M. Kaschner, O. Schillinger, T. Fettweiss, C. Nutschel, F. Krause, A. Fulton, B. Strodel, A. Stadler, K.-E. Jaeger, & U. Krauss
Sci. Rep., 7: 42592 (2017) [link]

Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains
M. Hora, M. Carballo Pacheco, B. Weber, V. K. Morris, A. Wittkopf, J. Buchner, B. Strodel & B. Reif
Sci. Rep., 7: 41515 (2017) [link]

Conformational Transitions of the Amyloid-β Peptide Upon Copper(II) Binding and pH Changes.
Q. Liao, M. C. Owen, O. O. Olubiyi, B. Barz, & B. Strodel
Israel J. Chem., 57: 771-784 (2017) [link]

Comparison of force fields for Alzheimer's Aβ42 : a case study for intrinsically disordered proteins.
M. Carballo Pacheco & B. Strodel
Protein Sci., 26: 174-185 (2017) [link]

Investigating structure and dynamics of Atg8 family proteins.
O. H. Weiergräber, M. Schwarten, B. Strodel & D. Willbold
Methods Enzymol., 587: 115-142 (2017) [link]

Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22
O. O. Olubiyi & B. Strodel
Data in Brief, 9, 642-647 (2016) [link]

A one-pot two-step hydroxylation of the macrocyclic diterpenoid β-cembrenediol catalyzed by P450 BM3 mutants
Le-Huu, D. Petrovic, B. Strodel & V. Urlacher
ChemCatChem, 8, 3755-3761 (2016) [link]

Radical Formation Initiates Solvent-Dependent Unfolding and β-Sheet Formation in a Model Helical Peptide
M. C. Owen, B. Strodel, I. G. Csizmadia & B. Viskolcz
J. Phys. Chem. B, 120, 4878-4889 (2016) [link]

Understanding Amyloid-β Oligomerization at the Molecular Level: the Role of the Fibril Surface.
B. Barz and B. Strodel
Chem Eur J, 22, 8768-8772 (2016) [link]

Characterization of Mn(II) ion Binding to the Amyloid-β Peptide in Alzheimer’s Disease
C. Wallin, Y.S. Kulkarni, A. Abelein, J. Jarvet, Q. Liao, B. Strodel, L. Olsson, J. Luo, J.P. Abrahams, S.B. Sholts, P.M. Roos, S.C.L. Kamerlin, A. Gräslund, S.K.T.S. Wärmländer
J Trace Elem Med Biol, DOI: 10.1016/j.jtemb.2016.03.009 (2016) [link]

Evaluation of the coarse-grained OPEP force field for protein-protein docking
P. Kynast, P. Derreumaux and B. Strodel
BMC Biophysics, 9:4 (2016) [link]

Advances in the Simulation of Protein Aggregation at the Atomistic Scale
M. Carballo-Pacheco and B. Strodel
J. Phys. Chem. B, 120, 2991–2999 (2016) [link]

An account of amyloid oligomers: facts and figures obtained from experiments and simulations
L. Nagel-Steger, M. C. Owen, and B. Strodel
ChemBioChem, 17, 657-676 (2016) [link]

Structural features determining thermal adaptation of esterases
F. Kovacic, A. Mandrysch, C. Poojari, B. Strodel, K.E. Jaeger
Protein Eng Des Sel., 29, 65-76 (2016) [link]

Conformational Polymorphism in Autophagy-Related Protein GATE-16
P. Ma, O. Schillinger, M. Schwarten, J. Lecher, R. Hartmann, M. Stoldt, J. Mohrlüder, O. Olubiyi, B. Strodel, D. Willbold, and O. H. Weiergräber.
Biochemistry, 54, 5469–5479 (2015) [link]

Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations
M. Carballo-Pacheco, A. Ismail, and B. Strodel.
J. Phys. Chem. B, 119, 9696-9705 (2015) [link]

Development and Application of a Nonbonded Cu2+ Model That Includes the Jahn–Teller Effect
Q. Liao, S.C.L. Kamerlin, and B. Strodel.
J. Phys. Chem. Lett., 6, 2657–2662 (2015) [link]

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies
Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Mai SL, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P.
Chem. Rev., 115, 3518-3563 (2015) [link]


Extension of the FACTS implicit solvation model to membranes
M. Carballo Pacheco, I. Vancea, and B. Strodel.
J. Chem. Theory Comput., 10, 3163-3176 (2014) [link]

Protein structure prediction: assembly of secondary structure elements by basin-hopping
F. Hoffmann, I. Vancea, S.G. Kamat, and B. Strodel.
Chem. Phys. Chem., 15, 3378–3390 (2014) [link]

Early amyloid β-protein aggregation precedes conformational change
B. Barz, O. Olubiyi, and B. Strodel.
Chem. Commun., 50, 5373-5375 (2014) [link]
This communication is part of themed collection: 2014 Emerging Investigators.

A Kinetic Approach to the Sequence–Aggregation Relationship in Disease-related Protein Assembly
B. Barz, D.J. Wales, and B. Strodel.
J. Phys. Chem. B., 118, 1003-1011 (2014) [link]

Book Review: Protein-Protein Interactions in Drug Discovery.
ChemBioChem, 15, 472-473 (2014) [link]

Amyloid aggregation inhibitory mechanism of arginine-rich D-peptides
O. Olubiyi, D. Frenzel, D. Bartnik, J.M. Glück, O. Brener, L. Nagel-Steger, S.A. Funke, D. Willbold, and B. Strodel.
Curr. Med. Chem., 21, 1448-1457 (2014) [link]


Interaction of Bcl-2 with the Autophagy-Related Protein GABARAP -- Biophysical Characterization and Functional Implications
Ma, P.; Schwarten, M.; Schneider, L.; Boeske, A.; Henke, N.; Lisak, D.; Weber, S.; Mohrluder, J.; Stoldt, M.; Strodel, B.; Methner, A.; Hoffmann, S.; Weiergraber, O. H.; Willbold, D.
J. Biol. Chem., 113, 1-26 (2013) [link]

Membrane permeation induced by aggregates of human islet amyloid polypeptides
C. Poojari, D. Xiao, V. S. Batista and B. Strodel.
Biophys. J., 105, 2323-2332 (2013) [link]

Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations
C. Poojari and B. Strodel.
PLoS ONE, 8: e78399 (2013) [link]

Thermodynamic analysis of structural transitions during GNNQQNY aggregation
K. L. Osborne, M. Bachmann and B. Strodel.
Proteins: Struct. Func. Bioinf., 81:1141–1155 (2013) [link]

Protein structure prediction using global optimization by basin-hopping with NMR shift restraints.
F. Hoffmann and B. Strodel.
J. Chem. Phys., 138:025102 (2013). [link]

How the amyloid-β peptide and membranes affect each other: an extensive simulation study.
C. Poojari, A. Kukol and B. Strodel.
BBA-Biomembranes, 1828, 327-339 (2013).[link]

Molecular modeling, dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 from Wuchereria bancrofti using cheminformatics and mutational studies.
O. P. Sharma, Y. Vadlamudi, Q. Liao, B. Strodel, and M. Suresh Kumar.
J. Biomol. Struct. Dyn., 31, 765-778 (2013).[link]


Structures of the Amyloid β-Peptides Aβ1-40 and Aβ1-42 as Influenced by pH and a D-Peptide
O.O. Olubiyi and B. Strodel.
J. Phys. Chem. B, 116, 3280-3291 (2012). [link]

Molecular modeling of human alkaline sphingomyelinase
P. S. Suresh, O. Olubiyi, C. Thirunavukkarasu, B. Strodel, M. S. Kumar
Bioinformation, 6, 78-82 (2011).[link]

Modelling Proteins: Conformational Sampling and Reconstruction of Folding Kinetics
K. Klenin, B. Strodel, D.J. Wales and W. Wenzel.
BBA-Proteins and Proteomics, 1814, 977-1000 (2011). [link]

Transmembrane structures for Alzheimer's Aβ1-42 oligomers.
B. Strodel, J.W.L. Lee, C.S. Whittleston and D.J. Wales.
J. Am. Chem. Soc., 132, 13300-13312 (2010). [link]

Interpolation Schemes for Peptide Rearrangements.
M.S. Bauer, B. Strodel, S.N. Fejer, E.F. Koslover and D.J. Wales.
J. Chem. Phys., 132, 054101 (2010). [link]

Symmetrisation of the AMBER and CHARMM Force Fields.
E. Malolepsza, B. Strodel, M. Khalili, S. Trygubenko, S. Fejer and D.J. Wales.
J. Comp. Chem., 31, 1402-1409 (2010). [link]

Frontiers Article: Free Energy Surfaces from an Extended Harmonic Superposition Approach and Kinetics for Alanine Dipeptide.
B. Strodel and D.J. Wales.
Chem. Phys. Lett., 466, 105-115 (2008). [link]

Characterising the first steps of amyloid formation for the ccβ peptide.
B. Strodel, A.W. Fitzpatrick, M. Vendruscolo, C.M. Dobson, and D.J. Wales.
J. Phys. Chem. B 112:9998-10004 (2008). [link]

Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide.
B. Strodel and D.J. Wales.
J. Chem. Theo. Comp. 4:657-672 (2008). [link]

Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide.
B. Strodel, C.S. Whittleston, and D.J. Wales.
J. Am. Chem. Soc. 129:16005-16014 (2007). [link]

Classical calculation of transient absorption spectra monitoring ultrafast electron transfer processes.
I. Uspenskiy, B. Strodel, and G. Stock.
J. Chem. Theo. Comp. 2:1605-1617 (2006). [link]

Classical description of the dynamics and time-resolved spectroscopy of nonadiabatic cis-trans photoisomerizations.
I. Uspenskiy, B. Strodel, and G. Stock.
Chem. Phys. 329:109-117 (2006). [link]

Quantum modeling of transient infrared spectra reflecting photoinduced electron-transfer dynamics.
B. Strodel and G. Stock.
J. Chem. Phys. 124:114105 (2006). [link]

Modeling of decoherence and dissipation in nonadiabatic photoreactions by an effective-scaling nonsecular Redfield algorithm.
B. Balzer and G. Stock.
Chem. Phys. 310:33-41 (2005). [link]

Transient spectral features of a cis-trans photoreaction in the condensed phase: A model study.
B. Balzer and G. Stock.
J. Phys. Chem. A 108:6464-6473 (2004). [link]

Mechanism of a photochemical funnel: a dissipative wave-packet dynamics study.
B. Balzer, S. Hahn, and G. Stock.
Chem. Phys. Lett. 379:351-358 (2003). [link]

Quasiclassical and semiclassical wave-packet dynamics n periodic potentials.
B. Balzer, S. Dilthey, G. Stock, and M. Thoss.
J. Chem. Phys. 119:5795-5804 (2003). [link]

Quasiperiodic orbit analysis of nonadiabatic cis-trans photoisomerization dynamics.
B. Balzer, S. Dilthey, S. Hahn, M. Thoss, and G. Stock.
J. Chem. Phys. 119:4204-4215, (2003). [link]

 Book Chapters and Proceedings

Functional Amyloids.
Carballo-Pacheco M., Barz B. and Strodel B. Proceedings of the 46th IFF Spring School Functional Soft Matter, 23 February - 06 March 2015, Jülich, Germany.

Thermodynamics and kinetics of amyloid aggregation from atomistic simulations.
Barz B. and Strodel B. Proceedings of the Conference Physical Biology of Proteins and Peptides: Theory, Experiment and Simulation, 18 - 20 February 2015, Mexico City, Mexico.

Thermodynamics of Protein Aggregation.
K. L. Osborne, B. Barz, M. Bachmann, and B. Strodel. Phys. Proc., 53, 90-95 (2014) [link]
Proceedings of the 26th Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics, Feb 25-Mar 1, 2013, Athens, Georgia, USA.

Secondary Structure Propensities of the Amyloid β-Peptide Aβ1−42 as Influenced by pH and a D-Peptide.
O. O. Olubiyi, B. Strodel.
In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 145-150 (2012).

Coarse Grained Simulation of Amyloid Aggregators.
K. Osborne, M. Bachmann, B. Strodel.
In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 151-155 (2012).

Modeling Transmembrane Amyloid-β Structures: Aβ–Membrane Interactions.
C. Poojari, B. Strodel.
In `From Computational Biophysics to Systems Biology (CBSB11)', Proceedings, 20-22 July 2011, Julich, Germany, ISBN 978-3-89336-748-1, pp. 157-162 (2012).

Pathways and Rates for Structural Transformations of Peptides and Proteins. In Energy Flow in Proteins.
D.J. Wales, J.M. Carr, M. Khalili, V. de Souza, B. Strodel, and C.S. Whittleston.
edited by D.Leitner and J.Straub, Taylor and Francis/CRC Press, 315-340 (2009). [link]