High-pressure NMR
2022
Dershwitz P, Gu W, Roche J, Kang-Yun C.S, Semrau J.D, Bobik T.A, Fulton B, Zischka H, DiSpirito A.A (2022) MbnC is not required for the formation of the N-terminal oxazolone in the methanobactin from Methylosinus trichosporium OB3b. Appli. Environ. Microbiol. 88: e01841-21
2021
Nguyen T. T, Ghirlando R, Roche J, Venditti V. (2021) Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity. Proc. Natl. Acad. Sci. USA. 118: e2100298118
2021
Nguyen T. T, Siang S, Roche J (2021) High-pressure NMR experiments for detecting protein low-lying conformational states. J. Vis. Exp 172: doi: 10.3791/62701
2021
Levengood J, Peterson J, Tolbert B, Roche J. (2021) Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 89:781-791
2019
Roche J. (2019) High-pressure NMR of biological systems in solution. eMagRes 8: 121-126
2019
Roche J, Royer C.A, Roumestand C. (2019) Exploring protein conformational landscapes using high-pressure NMR. Methods in Enzymology 614:293-320
2018
Roche J, Royer C.A (2018) Lessons from Pressure Denaturation of Proteins. J. R. Soc. Interface 15: pii 20180244
2017
Roche J. Royer C.A, Roumestand C. (2017) Monitoring protein folding through high pressure NMR. Prog. Nucl. Magn. Reson. Spectrosc. 102-103: 15-31
2017
Luan M. Nguyen, Roche J. (2017) High-pressure NMR techniques for the study of protein dynamics, folding and aggregation. J. Magn. Reson. 277: 179-185
2016
Louis J.M, Roche J. (2016) Evolution under drug pressure remodels the folding free-energy landscape of mature HIV-1 protease. J. Mol. Biol. 428: 2780-2792
2015
Roche J, Louis J.M, Bax A, Best R. (2015) "Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach". Proteins. 83: 2117-2123
2015
Tugarinov V, Libich D.A, Meyer V, Roche J, Clore G.M. (2015) "The energetics of a three-state protein folding system probed by high-pressure relaxation NMR from 1 to 2500 bar". Angew. Chem. Int. Ed. 54: 11157-11161
2013
Roche J, Dellarole M, Caro J.A, Norberto D.E, Garcia A.E, Garcia-Moreno B, Roumestand C, Royer C.A. (2013) "Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy". J. Am. Chem. Soc. 135: 14610-14618
2013
Roche J, Ying J, Maltsev A.S, Bax A. (2013) Impact of hydrostatic pressure on an intrinsically disordered protein: a high-pressure NMR study of a-synuclein. Chembiochem. 14: 1754-1761
2012
Roche J, Dellarole M, Caro J.A, Guca E, Norberto D.E, Yang T, Garcia A.E, Roumestand C, Garcia-Moreno B, Royer C.A. (2012) "Remodeling of the folding free-energy landscape of staphylococcal nuclease by cavity- creating mutations". Biochemistry 51: 9535-9546
2012
Roche J, Caro J.A, Norberto D.E, Barthe P, Roumestand C, Schlessman J.L, Garcia A.E, Garcia-Moreno B, Royer C.A. (2012) "Cavities determine the pressure unfolding of proteins". Proc. Natl. Acad. Sci. USA. 109: 6945-6950
2011
Rouget J-B, Aksel T, Roche J, Saldana J.L, Garcia A.E, Barrick D, Royer C.A. (2011) "Size and sequence and the volume change of protein folding". J. Am. Chem. Soc. 133: 6020-6027
2011
Kitahara R, Hata K, Maeno A, Akasaka K, Chimenti M.S, Garcia-Moreno B, Schroer M.A, Jeworrek C, Tolan M, Winter R, Roche J, Roumestand C, Montet de Guillen K, Royer C.A. (2011) "Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH". Proteins 79: 1293-1305
Scaffold proteins and disordered peptides involved in neurological diseases
2023
Kramer D.A, Narvaez-Ortiz, H.Y, Patel U, Shi R, Shen K, Nolen B.J, Roche J, Chen B. (2023) . (2023) The intrinsically disordered cytoplasmic tail of a dendrite branching receptor uses two distinct mechanisms to regulate the actin cytoskeleton. eLife 12: e88492
2022
Siang S, Underbakke E, Roche J (2022) Intricate coupling between the transactivation and basic-leucine zipper domains governs phosphorylation of transcription factor ATF4 by casein kinase 2. J. Biol. Chem 298: 101633
2021
Levengood J, Peterson J, Tolbert B, Roche J. (2021) Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 89:781-791
2019
Roche J, Potoyan D.A. (2019) Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained molecular dynamics simulations. J. Phys. Chem. B. 45: 9567-9575
2018
Baweja L, Roche J. (2018) Pushing the Limits of Structure-Based Models: Prediction of Non-globular Protein Folding and Fibrils Formation with Go-Model Simulations. J. Phys. Chem. B. DOI 10.1021/acs.jpcb.7b12129
2017
Shen Y, Roche J, Grishaev A, Bax A. (2017) Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins. Protein Sci. 27: 146-158
2016
Roche J, Ying J, Shen Y, Torchia D.A, Bax A. (2016) ARTSY-J: convenient and precise measurement of 3 J HNHa couplings in medium-size proteins from TROSY-HSQC spectra. J. Magn. Reson. 268: 73-81
2016
Roche J, Shen Y, Jung Ho L, Jinfa Y, Bax A. (2016) Monomeric Ab 1-40 and Ab 1-42 peptides in solution adopt very similar ramachandran map distributions that closely resemble random coil. Biochemistry 55: 762-775
2015
Roche J, Ying J, Bax A. (2015) Accurate measurement of 3 J HNHa couplings in small or disordered proteins from WATERGATE-optimized TROSY spectra. J. Biomol. NMR 64: 1-7
2014
Maltsev A.S, Grishaev A, Roche J, Zasloff M, Bax A. (2014) "Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase". J. Am. Chem. Soc. 136: 3752-3755
2013
Ying J, Roche J, Bax A. (2013) "Homonuclear decoupling for enhancing resolution and sensivity in NOE and RDC measurements of peptides and proteins". J. Magn. Reson. 241: 97-102
2013
Roche J, Ying J, Maltsev A.S, Bax A. (2013) Impact of hydrostatic pressure on an intrinsically disordered protein: a high-pressure NMR study of a-synuclein. Chembiochem. 14: 1754-1761
Evolution of viral proteins
2016
Agniswamy J, Louis J.M, Roche J, Harrison R.W, Weber I.T (2016) Structural studies of a rationally selected multi-drug resistant HIV-1 protease reveal synergistic effect of distal mutations on flap dynamics. PLoS One. 11: e0168616
2016
Louis J.M, Baber J.L, Ghirlando R, Aniana A, Bax A, Roche J. (2016) Insights into the conformation of the membrane proximal regions critical to the trimerization of the HIV-1 gp41 ectodomain bound to dodecyl phosphocholine micelles. PLoS One. 11: e0160597
2016
Louis J.M, Roche J. (2016) Evolution under drug pressure remodels the folding free-energy landscape of mature HIV-1 protease. J. Mol. Biol. 428: 2780-2792
2015
Roche J, Louis J.M, Aniana A, Ghirlando R, Bax A. (2015) Complete dissociation of the HIV-1 gp41 ectodomain and membrane proximal regions upon phospholipid binding. J. Biolmol. NMR 61: 235-248
2014
Roche J, Louis J.M, Bax A. (2014) Conformation of inhibitor-free HIV-1 protease derived from NMR spectroscopy in a weakly oriented solution. Chembiochem. 16: 214-218 ©
2014
Louis J.M, Aniana A, Lohith K, Sayer J.M, Roche J, Bewley C.A, Clore G.M. (2014) Binding of HIV-1 gp41-directed neutralizing and non-neutralizing fragment antibody binding domain (Fab) and single chain variable fragment (ScFv) antibodies to the ectodomain of gp41 in the pre-hairpin and six-helix bundle conformations. PLoS One. 9: e1046833
2014
Roche J, Louis J.M, Grishaev A, Ying J, Bax A. (2014) "Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion". Proc. Natl. Acad. Sci. USA. 111: 3425-3430
2013
Louis. J.M, Tozser J, Roche J, Matuz K, Aniana A, Sayer J.M. (2013) "Enhanced stability of monomer fold correlates with extreme drug resistance of HIV-1 Protease". Biochemistry 52: 7678-7688
Protein folding
2021
Nguyen T. T, Ghirlando R, Roche J, Venditti V. (2021) Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity. Proc. Natl. Acad. Sci. USA. 118: e2100298118
2021
Nguyen T. T, Siang S, Roche J (2021) High-pressure NMR experiments for detecting protein low-lying conformational states. J. Vis. Exp 172: doi: 10.3791/62701
2021
Levengood J, Peterson J, Tolbert B, Roche J. (2021) Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 89:781-791
2019
Roche J. (2019) High-pressure NMR of biological systems in solution. eMagRes 8: 121-126
2018
Baweja L, Roche J. (2018) Pushing the Limits of Structure-Based Models: Prediction of Non-globular Protein Folding and Fibrils Formation with Go-Model Simulations. J. Phys. Chem. B. DOI 10.1021/acs.jpcb.7b12129
2017
Roche J. Royer C.A, Roumestand C. (2017) Monitoring protein folding through high pressure NMR. Prog. Nucl. Magn. Reson. Spectrosc. 102-103: 15-31
2017
Luan M. Nguyen, Roche J. (2017) High-pressure NMR techniques for the study of protein dynamics, folding and aggregation. J. Magn. Reson. 277: 179-185
2015
Tugarinov V, Libich D.A, Meyer V, Roche J, Clore G.M. (2015) "The energetics of a three-state protein folding system probed by high-pressure relaxation NMR from 1 to 2500 bar". Angew. Chem. Int. Ed. 54: 11157-11161
2015
Dellarole M, Caro J.A, Roche J, Fossat M, Barthe P, Garcia-Moreno B, Royer C.A, Roumestand C (2015) "Evolutionarily conserved pattern of interactions in a protein revealed by local thermal expansion properties". J. Am. Chem. Soc. 137: 9354-9362
2013
Roche J, Dellarole M, Caro J.A, Norberto D.E, Garcia A.E, Garcia-Moreno B, Roumestand C, Royer C.A. (2013) "Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy". J. Am. Chem. Soc. 135: 14610-14618
2013
Dellarole M, Kobayashi K, Rouget J-B, Caro J.A, Roche J, Islam M.M, Garcia-Moreno B, Kuroda Y, Royer C.A. (2013) "Probing the physical determinants of thermal expansion of folded proteins". J. Phys. Chem. B. 117: 12742-12749
2013
Roche J, Caro J.A, Dellarole M, Guca E, Royer C.A, Garcia-Moreno B, Garcia A.E, Roumestand C. (2013) "Structural, energetic and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity- creating mutations". Proteins 81: 1069-1080
2012
Roche J, Dellarole M, Caro J.A, Guca E, Norberto D.E, Yang T, Garcia A.E, Roumestand C, Garcia-Moreno B, Royer C.A. (2012) "Remodeling of the folding free-energy landscape of staphylococcal nuclease by cavity- creating mutations". Biochemistry 51: 9535-9546
2012
Roche J, Caro J.A, Norberto D.E, Barthe P, Roumestand C, Schlessman J.L, Garcia A.E, Garcia-Moreno B, Royer C.A. (2012) "Cavities determine the pressure unfolding of proteins". Proc. Natl. Acad. Sci. USA. 109: 6945-6950
2011
Rouget J-B, Aksel T, Roche J, Saldana J.L, Garcia A.E, Barrick D, Royer C.A. (2011) "Size and sequence and the volume change of protein folding". J. Am. Chem. Soc. 133: 6020-6027
2023
Kramer D.A, Narvaez-Ortiz, H.Y, Patel U, Shi R, Shen K, Nolen B.J, Roche J, Chen B. (2023) . (2023) The intrinsically disordered cytoplasmic tail of a dendrite branching receptor uses two distinct mechanisms to regulate the actin cytoskeleton. eLife 12: e88492
2022
Siang S, Underbakke E, Roche J (2022) Intricate coupling between the transactivation and basic-leucine zipper domains governs phosphorylation of transcription factor ATF4 by casein kinase 2. J. Biol. Chem 298: 101633
Dershwitz P, Gu W, Roche J, Kang-Yun C.S, Semrau J.D, Bobik T.A, Fulton B, Zischka H, DiSpirito A.A (2022) MbnC is not required for the formation of the N-terminal oxazolone in the methanobactin from Methylosinus trichosporium OB3b. Appli. Environ. Microbiol. 88: e01841-21
2021
Nguyen T. T, Ghirlando R, Roche J, Venditti V. (2021) Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity. Proc. Natl. Acad. Sci. USA. 118: e2100298118
Nguyen T. T, Siang S, Roche J (2021) High-pressure NMR experiments for detecting protein low-lying conformational states. J. Vis. Exp 172: doi: 10.3791/62701
Levengood J, Peterson J, Tolbert B, Roche J. (2021) Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 89:781-791
2019
Roche J, Potoyan D.A. (2019) Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained molecular dynamics simulations. J. Phys. Chem. B. 45: 9567-9575
Roche J. (2019) High-pressure NMR of biological systems in solution. eMagRes 8: 121-126
Roche J, Royer C.A, Roumestand C. (2019) Exploring protein conformational landscapes using high-pressure NMR. Methods in Enzymology 614:293-320
2018
Roche J, Royer C.A (2018) Lessons from Pressure Denaturation of Proteins. J. R. Soc. Interface 15: pii 20180244
Baweja L, Roche J. (2018) Pushing the Limits of Structure-Based Models: Prediction of Non-globular Protein Folding and Fibrils Formation with Go-Model Simulations. J. Phys. Chem. B. DOI 10.1021/acs.jpcb.7b12129
2017
Shen Y, Roche J, Grishaev A, Bax A. (2017) Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins. Protein Sci. 27: 146-158
Roche J. Royer C.A, Roumestand C. (2017) Monitoring protein folding through high pressure NMR. Prog. Nucl. Magn. Reson. Spectrosc. 102-103: 15-31
Luan M. Nguyen, Roche J. (2017) High-pressure NMR techniques for the study of protein dynamics, folding and aggregation. J. Magn. Reson. 277: 179-185
2016
Agniswamy J, Louis J.M, Roche J, Harrison R.W, Weber I.T (2016) Structural studies of a rationally selected multi-drug resistant HIV-1 protease reveal synergistic effect of distal mutations on flap dynamics. PLoS One. 11: e0168616
Louis J.M, Baber J.L, Ghirlando R, Aniana A, Bax A, Roche J. (2016) Insights into the conformation of the membrane proximal regions critical to the trimerization of the HIV-1 gp41 ectodomain bound to dodecyl phosphocholine micelles. PLoS One. 11: e0160597
Louis J.M, Roche J. (2016) Evolution under drug pressure remodels the folding free-energy landscape of mature HIV-1 protease. J. Mol. Biol. 428: 2780-2792
Roche J, Ying J, Shen Y, Torchia D.A, Bax A. (2016) ARTSY-J: convenient and precise measurement of 3 J HNHa couplings in medium-size proteins from TROSY-HSQC spectra. J. Magn. Reson. 268: 73-81
Roche J, Shen Y, Jung Ho L, Jinfa Y, Bax A. (2016) Monomeric Ab 1-40 and Ab 1-42 peptides in solution adopt very similar ramachandran map distributions that closely resemble random coil. Biochemistry 55: 762-775
2015
Roche J, Ying J, Bax A. (2015) Accurate measurement of 3 J HNHa couplings in small or disordered proteins from WATERGATE-optimized TROSY spectra. J. Biomol. NMR 64: 1-7
Roche J, Louis J.M, Bax A, Best R. (2015) "Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach". Proteins. 83: 2117-2123
Tugarinov V, Libich D.A, Meyer V, Roche J, Clore G.M. (2015) "The energetics of a three-state protein folding system probed by high-pressure relaxation NMR from 1 to 2500 bar". Angew. Chem. Int. Ed. 54: 11157-11161
Dellarole M, Caro J.A, Roche J, Fossat M, Barthe P, Garcia-Moreno B, Royer C.A, Roumestand C (2015) "Evolutionarily conserved pattern of interactions in a protein revealed by local thermal expansion properties". J. Am. Chem. Soc. 137: 9354-9362
Roche J, Louis J.M, Aniana A, Ghirlando R, Bax A. (2015) Complete dissociation of the HIV-1 gp41 ectodomain and membrane proximal regions upon phospholipid binding. J. Biolmol. NMR 61: 235-248
2014
Roche J, Louis J.M, Bax A. (2014) Conformation of inhibitor-free HIV-1 protease derived from NMR spectroscopy in a weakly oriented solution. Chembiochem. 16: 214-218 ©
Louis J.M, Aniana A, Lohith K, Sayer J.M, Roche J, Bewley C.A, Clore G.M. (2014) Binding of HIV-1 gp41-directed neutralizing and non-neutralizing fragment antibody binding domain (Fab) and single chain variable fragment (ScFv) antibodies to the ectodomain of gp41 in the pre-hairpin and six-helix bundle conformations. PLoS One. 9: e1046833
Maltsev A.S, Grishaev A, Roche J, Zasloff M, Bax A. (2014) "Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase". J. Am. Chem. Soc. 136: 3752-3755
Roche J, Louis J.M, Grishaev A, Ying J, Bax A. (2014) "Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion". Proc. Natl. Acad. Sci. USA. 111: 3425-3430
2013
Ying J, Roche J, Bax A. (2013) "Homonuclear decoupling for enhancing resolution and sensivity in NOE and RDC measurements of peptides and proteins". J. Magn. Reson. 241: 97-102
Louis. J.M, Tozser J, Roche J, Matuz K, Aniana A, Sayer J.M. (2013) "Enhanced stability of monomer fold correlates with extreme drug resistance of HIV-1 Protease". Biochemistry 52: 7678-7688
Roche J, Dellarole M, Caro J.A, Norberto D.E, Garcia A.E, Garcia-Moreno B, Roumestand C, Royer C.A. (2013) "Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy". J. Am. Chem. Soc. 135: 14610-14618
Roche J, Ying J, Maltsev A.S, Bax A. (2013) Impact of hydrostatic pressure on an intrinsically disordered protein: a high-pressure NMR study of a-synuclein. Chembiochem. 14: 1754-1761
Dellarole M, Kobayashi K, Rouget J-B, Caro J.A, Roche J, Islam M.M, Garcia-Moreno B, Kuroda Y, Royer C.A. (2013) "Probing the physical determinants of thermal expansion of folded proteins". J. Phys. Chem. B. 117: 12742-12749
Roche J, Caro J.A, Dellarole M, Guca E, Royer C.A, Garcia-Moreno B, Garcia A.E, Roumestand C. (2013) "Structural, energetic and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity- creating mutations". Proteins 81: 1069-1080
2012
Roche J, Dellarole M, Caro J.A, Guca E, Norberto D.E, Yang T, Garcia A.E, Roumestand C, Garcia-Moreno B, Royer C.A. (2012) "Remodeling of the folding free-energy landscape of staphylococcal nuclease by cavity- creating mutations". Biochemistry 51: 9535-9546
Roche J, Caro J.A, Norberto D.E, Barthe P, Roumestand C, Schlessman J.L, Garcia A.E, Garcia-Moreno B, Royer C.A. (2012) "Cavities determine the pressure unfolding of proteins". Proc. Natl. Acad. Sci. USA. 109: 6945-6950
2011
Rouget J-B, Aksel T, Roche J, Saldana J.L, Garcia A.E, Barrick D, Royer C.A. (2011) "Size and sequence and the volume change of protein folding". J. Am. Chem. Soc. 133: 6020-6027
Kitahara R, Hata K, Maeno A, Akasaka K, Chimenti M.S, Garcia-Moreno B, Schroer M.A, Jeworrek C, Tolan M, Winter R, Roche J, Roumestand C, Montet de Guillen K, Royer C.A. (2011) "Structural plasticity of staphylococcal nuclease probed by perturbation with pressure and pH". Proteins 79: 1293-1305