Ran Friedman
Professor
Institutionen för kemi och biomedicin
Fakulteten för hälso- och livsvetenskap
Jag är professor i kemi med inriktning mot beräkningskemi och biokemi. Jag undervisar mest i fysikalisk kemi och läkemedelskemi. I min forskning sysslar jag med beräkningskemi, som betyder att jag studerar kemi med hjälp av beräkningar och simuleringar.
Undervisning
Jag undervisar vid kemi hos olika kurser och nivåer, och för olika studenter. Jag är involverad i undervisning framför allt för studenter inom livsmedelsvetenskap programmet och farmaceutprogrammet där undervisar jag läkemedelskemi. Dessutom undervisar jag ibland också masterstudenter och även doktorander.
Forskning
Forskningen fokuserar på beräkningskemi med inriktning på biomolekyler. Jag vill vidga förståelsen för de molekylära aspekterna av sjukdomsrelaterad amyloid aggregation genom simulering, konstruktion av hämmare som potentiella antimalariaföreningar, och grundläggande studier av interaktion jon-protein.
Jag använder sig av molekyldynamiksimuleringar, datorstödd läkemedelsdesign, kvantkemi, grovkorniga modeller, kontinuum-elektrostatik och andra molekylmodelleringsmetoder för att uppnå dessa mål, och har specialkunskaper i s k essential dynamics sampling (för acceleration av molekyldynamikstudier) och energisönderfallsanalys i kvantumkemi. Aktuellt fokus ligger på amyloid aggregation och interaktion makromolekyler-joner.
Mina forskargrupper
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Computational Chemistry and Biochemistry Group Vi använder datorsimuleringar för att bättre förstå hur biologiskt relevanta och andra intressanta molekyler beter sig. Bland annat studerar vi varför en…
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Linnaeus University Centre for Biomaterials Chemistry Linnéuniversitetets spetsforskningsgrupp inom området biomaterialkemi arbetar med utveckling och tillämpning av material som kan efterlikna…
Mina pågående forskningsprojekt
Publikationer
Artikel i tidskrift (Refereegranskat)
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Lindahl, E., Arvidsson, E., Friedman, R. (2024). Trans vs Cis : A Computational Study of Enasidenib Resistance due to IDH2 Mutations. Physical Chemistry, Chemical Physics - PCCP. 26 (27). 18989-18996.
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Lindström, H.J.G., De Wijn, A.S., Friedman, R. (2024). Interplay of mutations, alternate mechanisms, and treatment breaks in leukaemia : Understanding and implications studied with stochastic models. Computers in Biology and Medicine. 169.
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Freire, T.S., Zukerman-Schpector, J., Friedman, R., Caracelli, I. (2024). Structural and thermodynamic characterization of allosteric transitions in human serum albumin with metadynamics simulations. Physical Chemistry, Chemical Physics - PCCP. 26 (7). 6436-6447.
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Yang, J., Friedman, R. (2024). Synergy and antagonism between azacitidine and FLT3 inhibitors. Computers in Biology and Medicine. 169. 107889-107889.
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Freire, T.S., Caracelli, I., Zukerman-Schpector, J., Friedman, R. (2023). Resistance to a tyrosine kinase inhibitor mediated by changes to the conformation space of the kinase. Physical Chemistry, Chemical Physics - PCCP. 25 (8). 6175-6183.
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Friedman, R. (2023). Estimating the Gibbs Hydration Energies of Actinium and Trans-Plutonium Actinides. ChemPhysChem. 24 (2).
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Meelua, W., Wanjai, T., Thinkumrob, N., Friedman, R., Jitonnom, J. (2023). Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1‑OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1. Journal of Chemical Information and Modeling. 63 (15). 4827-4838.
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Månsson, A., Ušaj, M., Moretto, L., Matusovsky, O., Velayuthan, L.P., et al. (2023). New paradigms in actomyosin energy transduction : Critical evaluation of non-traditional models for orthophosphate release. Bioessays. 45 (9).
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Yang, J., Friedman, R. (2023). Combination strategies to overcome drug resistance in FLT+ acute myeloid leukaemia. Cancer Cell International. 23 (1).
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Oruganti, B., Lindahl, E., Yang, J., Amiri, W., Rahimullah, R., et al. (2022). Allosteric enhancement of the BCR-Abl1 kinase inhibition activity of nilotinib by cobinding of asciminib. Journal of Biological Chemistry. 298 (8).
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Lindström, J., Friedman, R. (2022). Rotating between ponatiniband imatinib temporarily increasesthe efficacy of imatinib as shownin a chronic myeloid leukaemiamodel. Scientific Reports. 12.
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Xu, Y., Zhang, S., Lindahl, E., Friedman, R., Wu, W., et al. (2022). A general tight-binding based energy decomposition analysis scheme for intermolecular interactions in large molecules. Journal of Chemical Physics. 157 (3).
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Friedman, R. (2022). The molecular mechanisms behind activation of FLT3 in acute myeloid leukemia and resistance to therapy by selective inhibitors. Biochimica et Biophysica Acta. CR. Reviews on Cancer. 1877 (1).
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Moretto, L., Ušaj, M., Matusovsky, O., Rassier, D.E., Friedman, R., et al. (2022). Multistep orthophosphate release tunes actomyosin energy transduction. Nature Communications. 13 (1).
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Friedman, R. (2022). Computational studies of protein–drug binding affinity changes upon mutations in the drug target. WIREs Computational Molecular Science. 12 (1).
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Xu, Y., Friedman, R., Wu, W., Su, P. (2021). Understanding intermolecular interactions of large systems in ground state and excited state by using density functional based tight binding methods. Journal of Chemical Physics. 154 (19).
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Yang, J., Lindström, J., Friedman, R. (2021). Combating drug resistance in acute myeloid leukaemia by drug rotations : the effects of quizartinib and pexidartinib. Cancer Cell International. 21 (1).
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Oruganti, B., Friedman, R. (2021). Activation of Abl1 Kinase Explored Using Well-Tempered Metadynamics Simulations on an Essential Dynamics Sampled Path. Journal of Chemical Theory and Computation. 17 (11). 7260-7270.
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Friedman, R. (2021). Preferential Binding of Lanthanides to Methanol Dehydrogenase Evaluated with Density Functional Theory. Journal of Physical Chemistry B. 125 (9). 2251-2257.
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Lindström, J., Friedman, R. (2020). Inferring time-dependent population growth rates in cell cultures undergoing adaptation. BMC Bioinformatics. 21 (1). 1-13.
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Houshmand, F., Friedman, R., Jalili, S., Schofield, J. (2020). Exciton effect in new generation of carbon nanotubes : graphdiyne nanotubes. Journal of Molecular Modeling. 26 (7). 1-10.
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Todde, G., Friedman, R. (2020). Pattern and Dynamics of FLT3 Duplications. Journal of Chemical Information and Modeling. 60 (8). 4005-4020.
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Lindström, J., Friedman, R. (2020). The effects of combination treatments on drug resistance in chronic myeloid leukaemia : an evaluation of the tyrosine kinase inhibitors axitinib and asciminib. BMC Cancer. 20 (1).
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Buetti-Dinh, A., Herold, M., Christel, S., El Hajjami, M., Delogu, F., et al. (2020). Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. BMC Bioinformatics. 21 (1). 1-15.
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Georgoulia, P.S., Bjelic, S., Friedman, R. (2020). Deciphering the molecular mechanism of FLT3 resistance mutations. The FEBS Journal. 287 (15). 3200-3220.
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Davila-Rodriguez, M.J., Freire, T.S., Lindahl, E., Caracelli, I., Zukerman-Schpector, J., et al. (2020). Is breaking of a hydrogen bond enough to lead to drug resistance?. Chemical Communications. 56 (49). 6727-6730.
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Georgoulia, P.S., Todde, G., Bjelic, S., Friedman, R. (2019). The catalytic activity of Abl1 single and compound mutations : Implications for the mechanism of drug resistance mutations in chronic myeloid leukaemia. Biochimica et Biophysica Acta - General Subjects. 1863 (4). 732-741.
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Todde, G., Friedman, R. (2019). Activation and Inactivation of the FLT3 Kinase: Pathway Intermediates and the Free Energy of Transition. Journal of Physical Chemistry B. 123 (26). 5385-5394.
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Lindström, J., De Wijn, A.S., Friedman, R. (2019). Stochastic modelling of tyrosine kinase inhibitor rotation therapy in chronic myeloid leukaemia. BMC Cancer. 19. 1-13.
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Steinz, M.M., Persson, M., Aresh, B., Olsson, K., Cheng, A.J., et al. (2019). Oxidative hotspots on actin promote skeletal muscle weakness in rheumatoid arthritis. JCI Insight. 4 (9). 1-16.
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Friedman, R. (2019). Specific Ion and Concentration Effects in Acetate Solutions with Na+, K+ and Cs+. ChemPhysChem. 20 (8). 1006-1010.
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Gagner, V.A., Lundholm, I., Garcia-Bonete, M., Rodilla, H., Friedman, R., et al. (2019). Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties. Scientific Reports. 9. 1-14.
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Friedman, R. (2019). Simulations of Biomolecules in Electrolyte Solutions. Advanced Theory and Simulations. 2 (4). 1-10.
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Todde, G., Friedman, R. (2019). Conformational modifications induced by internal tandem duplications on the FLT3 kinase and juxtamembrane domains. Physical Chemistry, Chemical Physics - PCCP. 21 (34). 18467-18476.
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Buetti-Dinh, A., Friedman, R. (2018). Computer simulations of the signalling network in FLT3+-acute myeloid leukaemia : indications for an optimal dosage of inhibitors against FLT3 and CDK6. BMC Bioinformatics. 19. 1-13.
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Friedman, R. (2018). Membrane-Ion Interactions. Journal of Membrane Biology. 251 (3). 453-460.
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Ahlstrand, E., Buetti-Dinh, A., Friedman, R. (2018). An interactive computer lab of the galvanic cell for students in biochemistry. Biochemistry and molecular biology education. 46 (1). 58-65.
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Buetti-Dinh, A., Jensen, R., Friedman, R. (2018). A computational study of hedgehog signalling involved in basal cell carcinoma reveals the potential and limitation of combination therapy. BMC Cancer. 18 (1). 1-8.
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Friedman, R. (2017). The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib. Proteins : Structure, Function, and Bioinformatics. 85 (11). 2143-2152.
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Ahlstrand, E., Hermansson, K., Friedman, R. (2017). Interaction Energies in Complexes of Zn and Amino Acids : A Comparison of Ab Initio and Force Field Based Calculations. Journal of Physical Chemistry A. 121 (13). 2643-2654.
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Karlsson, B.C.G., Friedman, R. (2017). Dilution of whisky - the molecular perspective. Scientific Reports. 7 (6489).
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Ahlstrand, E., Zukerman Schpector, J., Friedman, R. (2017). Computer simulations of alkali-acetate solutions : Accuracy of the forcefields in difference concentrations. Journal of Chemical Physics. 147. 1-10.
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Becconi, O., Ahlstrand, E., Salis, A., Friedman, R. (2017). Protein-ion Interactions : Simulations of Bovine Serum Albumin in Physiological Solutions of NaCl, KCl and LiCl. Israel Journal of Chemistry. 57 (5). 403-412.
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Maganhi, S.H., Jensen, P., Caracelli, I., Schpector, J.Z., Froehling, S., et al. (2017). Palbociclib can overcome mutations in cyclin dependent kinase 6 that break hydrogen bonds between the drug and the protein. Protein Science. 26 (4). 870-879.
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Pineda De Castro, L.F., Dopson, M., Friedman, R. (2016). Biological Membranes in Extreme Conditions : Anionic Tetraether Lipid Membranes and Their Interactions with Sodium and Potassium. Journal of Physical Chemistry B. 120 (41). 10628-10634.
Status: Publicerad -
Buetti-Dinh, A., O'hare, T., Friedman, R. (2016). Sensitivity Analysis of the NPM-ALK Signalling Network Reveals Important Pathways for Anaplastic Large Cell Lymphoma Combination Therapy. PLOS ONE. 11 (9).
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Friedman, R. (2016). Drug resistance in cancer : molecular evolution and compensatory proliferation. Oncotarget. 7 (11). 11746-11755.
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Buetti-Dinh, A., Dethlefsen, O., Friedman, R., Dopson, M. (2016). Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes. Microbiology. 162 (8). 1422-1434.
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Pineda De Castro, L.F., Dopson, M., Friedman, R. (2016). Biological Membranes in Extreme Conditions : Simulations of Anionic Archaeal Tetraether Lipid Membranes. PLOS ONE. 11 (5).
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Lundholm, I.V., Rodilla, H., Wahlgren, W.Y., Duelli, A., Bourenkov, G., et al. (2015). Terahertz radiation induces non-thermal structural changes associated with Fröhlich condensation in a protein crystal. Structural Dynamics. 2 (5).
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Cournia, Z., Allen, T.W., Andricioaei, I., Antonny, B., Baum, D., et al. (2015). Membrane Protein Structure, Function, and Dynamics : a Perspective from Experiments and Theory. Journal of Membrane Biology. 248 (4). 611-640.
Status: Publicerad -
Buetti-Dinh, A., Pivkin, I., Friedman, R. (2015). S100A4 and its role in metastasis – computational integration of data on biological networks. Molecular Biosystems. 11. 2238-2246.
Status: Publicerad -
Chavan, S., Friedman, R., Nicholls, I.A. (2015). Acute Toxicity-Supported Chronic Toxicity Prediction: A k-Nearest Neighbor Coupled Read-Across Strategy. International Journal of Molecular Sciences. 16 (5). 11659-11677.
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Buetti-Dinh, A., Pivkin, I.V., Friedman, R. (2015). S100A4 and its role in metastasis : simulations of knockout and amplification of epithelial growth factor receptor and matrix metalloproteinases. Molecular Biosystems. 11 (8). 2247-2254.
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Friedman, R. (2014). Structural and computational insights into the versatility of cadmium binding to proteins. Dalton Transactions. 43 (7). 2878-2887.
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Friedman, R., Caflisch, A. (2014). Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends : A simulation study. Proteins : Structure, Function, and Bioinformatics. 82 (3). 399-404.
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Zabriskie, M.S., Eide, C.A., Tantravahi, S.K., Vellore, N.A., Estrada, J., et al. (2014). BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia. Cancer Cell. 26 (3). 428-442.
Status: Publicerad -
Friedman, R. (2013). Electrolyte Solutions and Specific Ion Effects on Interfaces. Journal of Chemical Education. 90 (8). 1018-1023.
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Friedman, R. (2013). Drug Resistance Missense Mutations in Cancer Are Subject to Evolutionary Constraints. PLOS ONE. 8 (12).
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Karlsson, B.C.G., Olsson, G.D., Friedman, R., Rosengren, A.M., Henschel, H., et al. (2013). How warfarin’s structural diversity influences its phospholipid bilayer membrane permeation. Journal of Physical Chemistry B. 117 (8). 2384-2395.
Status: Publicerad -
Ahlstrand, E., Spångberg, D., Hermansson, K., Friedman, R. (2013). Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands. International Journal of Quantum Chemistry. 113 (23). 2554-2562.
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Friedman, R. (2011). Aggregation of amyloids in a cellular context : modelling and experiment. Biochemical Journal. 438. 415-426.
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Friedman, R., Caflisch, A. (2011). Surfactant Effects on Amyloid Aggregation Kinetics. Journal of Molecular Biology. 414. 303-312.
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Seeber, M., Felline, A., Raimondi, F., Muff, S., Friedman, R., et al. (2011). Wordom : a user-friendly program for the analysis of molecular conformations, trajectories, and free energy surfaces. Journal of Computational Chemistry. 32 (6). 1183-1194.
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Friedman, R. (2011). Ions and the protein surface revisited : extensive molecular dynamics simulations and analysis of protein structures in alkali-chloride solutions. Journal of Physical Chemistry B. 115. 9213-9223.
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Friedman, R., Pellarin, R., Caflisch, A. (2010). Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles. The Journal of Physical Chemistry Letters. 1 (2). 471-474.
Status: Publicerad -
Friedman, R., Caflisch, A. (2010). On the orientation of the catalytic dyad in aspartic proteases. Proteins : Structure, Function, and Bioinformatics. 78 (6). 1575-1582.
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Friedman, R., Caflisch, A. (2009). Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. ChemMedChem. 4 (8). 1317-1326.
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Friedman, R., Pellarin, R., Caflisch, A. (2009). Amyloid aggregation on lipid bilayers and its impact on membrane permeability. Journal of Molecular Biology. 387 (2). 407-415.
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Friedman, R. (2009). Proton Transfer on the Molecular Surface of Proteins and Model Systems. Israel Journal of Chemistry. 49 (2). 149-153.
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Dashevskaya, S., Kopito, R.B., Friedman, R., Elbaum, M., Epel, B.L. (2008). Diffusion of anionic and neutral GFP derivatives through plasmodesmata in epidermal cells of Nicotiana benthamiana. Protoplasma.
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Friedman, R., Caflisch, A. (2008). Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins : Structure, Function, and Bioinformatics. 73 (4). 814-827.
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Friedman, R., Fischer, S., Nachliel, E., Scheiner, S., Gutman, M. (2007). Minimum energy pathways for proton transfer between adjacent sites exposed to water. Journal of Physical Chemistry B. 111 (21). 6059-6070.
Status: Publicerad -
Tsfadia, Y., Friedman, R., Kadmon, J., Selzer, A., Nachliel, E., et al. (2007). Molecular dynamics simulations of palmitate entry into the hydrophobic pocket of the fatty acid binding protein. FEBS Letters. 581. 1243-1247.
Status: Publicerad -
Friedman, R. (2007). Myosin V movement : Lessons from molecular dynamics studies of IQ peptides in the lever arm. Biochemistry. 46 (50). 14524-14536.
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Friedman, R., Caflisch, A. (2007). The Protonation State of the Catalytic Aspartates in Plasmepsin II. FEBS Letters. 581. 4120-4124.
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Friedman, R., Nachliel, E., Gutman, M. (2006). Fatty Acid Binding Proteins - Same Structure but Different Binding Mechanisms? : Molecular Dynamics Simulations of Intestinal Fatty Acid Binding Protein. Biophysical Journal. 90. 1535-45.
Status: Publicerad -
Gutman, M., Nachliel, E., Friedman, R. (2006). The dynamics of proton transfer between adjacent sites. Photochemical and Photobiological Sciences. 5. 531-537.
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Project, E., Friedman, R., Nachliel, E., Gutman, M. (2006). A Molecular Dynamics Study of the Effect of Ca2+ Removal on Calmodulin Structure. Biophys. J.. 90. 3842-3850.
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Ganoth, A., Friedman, R., Nachliel, E., Gutman, M. (2006). A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides. Biophysical Journal. 91 (7). 2436-2450.
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Gutman, M., Nachliel, E., Friedman, R. (2006). The mechanism of proton transfer between adjacent sites on the molecular surface. Biochimica et Biophysica Acta. 1757. 931-941.
Status: Publicerad -
Ganoth, A., Nachliel, E., Friedman, R., Gutman, M. (2006). Molecular dynamics study of a calmodulin-like protein with an IQ peptide : spontaneous refolding of the protein around the peptide. Proteins : Structure, Function, and Bioinformatics. 64 (1). 133-146.
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Mezer, A., Friedman, R., Noivirt, O., Nachliel, E., Gutman, M. (2005). The mechanism of proton transfer between adjacent sites exposed to water. J. Chem. Phys. B. 109. 11379-11388.
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Friedman, R., Nachliel, E., Gutman, M. (2005). Molecular Dynamics of a Protein Surface : Ion-Residues Interactions. Biophysical Journal. 89 (2). 768-781.
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Friedman, R., Nachliel, E., Gutman, M. (2005). Application of Classical Molecular Dynamics for Evaluation of Proton Transfer Mechanism on a Protein. Bioch. Bioph. Acta.. 1710. 67-77.
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Friedman, R., Nachliel, E., Gutman, M. (2005). Protein surface dynamics : Interaction with water and small solutes. Journal of biological physics (Print). 31 (3). 433-452.
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Friedman, R., Nachliel, E., Gutman, M. (2005). Molecular Dynamics Simulations of the Adipocyte Lipid Binding Protein Reveal a Novel Entry Site for the Ligand. Biochemistry. 44. 4275-4283.
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Friedman, R., Nachliel, E., Gutman, M. (2005). Protein Surface - the Dynamics of the Interactions between Protein, Water and Small Solutes. Journal of biological physics (Print). 31 (3-4). 433-452.
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Friedman, R., Nachliel, E., Gutman, M. (2003). The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. Biophysical Journal. 85 (2). 886-896.
Status: Publicerad
Konferensbidrag (Refereegranskat)
- Steinz, M., Malin, P., Bejan, A., Cheng, A., Ahlstrand, E., et al. (2018). Identification of oxidative hotspots on actin which promote skeletal muscle weakness in rheumatoid arthritis. Free Radical Biology and Medicine. S106.
- Katona, G., Lundholm, I., Rodilla, H., Garcia-Bonete, M., Duelli, A., et al. (2016). Bayesian analysis of non-thermal structural changes induced by terahertz radiation in protein crystals. 2016 41ST INTERNATIONAL CONFERENCE ON INFRARED, MILLIMETER, AND TERAHERTZ WAVES (IRMMW-THZ).
Kapitel i bok, del av antologi (Refereegranskat)
- Friedman, R. (2024). The Emerging Role of Molecular Dynamics Simulations in Cancer Research. Comprehensive Computational Chemistry : Molecular Dynamics Simulations and Reaction Rates. Oxford. UK, Elsevier. 910-920.
Artikel, forskningsöversikt (Refereegranskat)
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Friedman, R., Bjelic, S. (2020). Simulations Studies of Protein Kinases that are Molecular Targets in Cancer. Israel Journal of Chemistry. John Wiley & Sons. 60 (7). 667-680.
Status: Publicerad -
Friedman, R., Khalid, S., Aponte-Santamaria, C., Arutyunova, E., Becker, M., et al. (2018). Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology. Journal of Membrane Biology. Springer. 251 (5-6). 609-631.
Status: Publicerad -
Friedman, R., Boye, K., Flatmark, K. (2013). Molecular modelling and simulations in cancer research. Biochimica et Biophysica Acta. CR. Reviews on Cancer. 1836 (1). 1-14.
Status: Publicerad
Artikel i tidskrift (Övrigt vetenskapligt)
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Friedman, R., Agmon, N. (2017). Charge Transfer in Proteins : In Celebration of Hemi Gutman's 80th Birthday. Israel Journal of Chemistry. 57 (5). 355-356.
Status: Publicerad