Publications
O. Mikhailovskii, S.A. Izmailov, Y. Xue, D.A. Case, N.R. Skrynnikov,
X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals,
J Chem Inf Model 64 (2024) 18–25.
https://doi.org/10.1021/acs.jcim.3c01531
O.O. Lebedenko, V.A. Salikov, S.A. Izmailov, I.S. Podkorytov, N.R. Skrynnikov,
Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4,
Biophys J. (2023) S0006-3495(23)00720–8.
https://doi.org/10.1016/j.bpj.2023.11.020
W. Sun, O.O. Lebedenko, N.G. Salguero, M.D. Shannon, M. Zandian, M.G. Poirier, N.R. Skrynnikov, C.P. Jaroniec,
Conformational and Interaction Landscape of Histone H4 Tails in Nucleosomes Probed by Paramagnetic NMR Spectroscopy,
J. Am. Chem. Soc. 145 (2023) 25478–25485.
https://doi.org/10.1021/jacs.3c10340
D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda,
Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,
J Struct Biol X. 7 (2023) 100079.
https://doi.org/10.1016/j.yjsbx.2022.100079
N. Liu, O. Mikhailovskii, N.R. Skrynnikov, Y. Xue,
Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography,
IUCrJ. 10 (2023) 16–26.
https://doi.org/10.1107/S2052252522011198
I.S. Podkorytov, N.R. Skrynnikov,
Effect of rotation in NMR diffusion experiments on micron-sized particles: A generalized theoretical treatment,
J Magn Reson. 344 (2022) 107303.
https://doi.org/10.1016/j.jmr.2022.107303
S.D.E. Fried, K.S.K. Hewage, A.R. Eitel, A.V. Struts, N. Weerasinghe, S.M.D.C. Perera, M.F. Brown,
Hydration-mediated G-protein-coupled receptor activation,
Proc Natl Acad Sci U S A. 119 (2022) e2117349119.
https://doi.org/10.1073/pnas.2117349119
B. Kharkov, X. Duan, J. Rantaharju, M. Sabba, M.H. Levitt, J.W. Canary, A. Jerschow,
Weak nuclear spin singlet relaxation mechanisms revealed by experiment and computation,
Phys Chem Chem Phys. 24 (2022) 7531–7538.
https://doi.org/10.1039/d1cp05537b
O. Mikhailovskii, Y. Xue, N.R. Skrynnikov,
Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber,
IUCrJ. 9 (2022) 114–133.
https://doi.org/10.1107/S2052252521011891
D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022),
Amber 2022,
University of California, San Francisco
https://ambermd.org/doc12/Amber22.pdf
DOI: 10.13140/RG.2.2.31337.77924
N.R. Skrynnikov,
Toward a proper interpretation of hydrogen exchange data in disordered proteins,
Biophys J. 120 (2021) 3855–3856.
https://doi.org/10.1016/j.bpj.2021.08.004
B.B. Kharkov, I.S. Podkorytov, S.A. Bondarev, M.V. Belousov, V.A. Salikov, G.A. Zhouravleva, N.R. Skrynnikov,
The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils,
Angew Chem Int Ed Engl. 60 (2021) 15445–15451.
https://doi.org/10.1002/anie.202102408
S.O. Rabdano, M.D. Shannon, S.A. Izmailov, N. Gonzalez Salguero, M. Zandian, R.N. Purusottam, M.G. Poirier, N.R. Skrynnikov, C.P. Jaroniec,
Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA,
Angew Chem Int Ed Engl. 60 (2021) 6480–6487.
https://doi.org/10.1002/anie.202012046
M.J. Sheedlo, S. Kenny, I.S. Podkorytov, K. Brown, J. Ma, S. Iyer, C.S. Hewitt, T. Arbough, O. Mikhailovskii, D.P. Flaherty, M.A. Wilson, N.R. Skrynnikov, C. Das,
Insights into Ubiquitin Product Release in Hydrolysis Catalyzed by the Bacterial Deubiquitinase SdeA,
Biochemistry. 60 (2021) 584–596.
https://doi.org/10.1021/acs.biochem.0c00760
U. Chawla, S.M.D.C. Perera, S.D.E. Fried, A.R. Eitel, B. Mertz, N. Weerasinghe, M.C. Pitman, A.V. Struts, M.F. Brown,
Activation of the G-Protein-Coupled Receptor Rhodopsin by Water,
Angew Chem Int Ed Engl. 60 (2021) 2288–2295.
https://doi.org/10.1002/anie.202003342
D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, C. Jin, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2021),
Amber 2021,
University of California, San Francisco
https://ambermd.org/doc12/Amber21.pdf
DOI: 10.13140/RG.2.2.15902.66881
S.A. Izmailov, S.O. Rabdano, Z. Hasanbasri, I.S. Podkorytov, S. Saxena, N.R. Skrynnikov,
Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories,
Sci Rep. 10 (2020) 957.
https://doi.org/10.1038/s41598-019-56750-y
D.A. Luzik, O.N. Rogacheva, S.A. Izmailov, M.I. Indeykina, A.S. Kononikhin, N.R. Skrynnikov,
Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2,
Sci Rep. 9 (2019) 20219.
https://doi.org/10.1038/s41598-019-56078-7
M.N. Ryazantsev, D.M. Nikolaev, A.V. Struts, M.F. Brown,
Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins,
J Membr Biol. 252 (2019) 425–449.
https://doi.org/10.1007/s00232-019-00095-0
A.A. Titov, O.A. Filippov, A.F. Smol’yakov, I.A. Godovikov, J.R. Shakirova, S.P. Tunik, I.S. Podkorytov, E.S. Shubina,
Luminescent Complexes of the Trinuclear Silver(I) and Copper(I) Pyrazolates Supported with Bis(diphenylphosphino)methane,
Inorg Chem. 58 (2019) 8645–8656.
https://doi.org/10.1021/acs.inorgchem.9b00991
I.S. Podkorytov, T.G. Cherkasova, E.A. Kayfadzhyan, Yu.S. Varshavsky,
Multiplet-Matched Filtering of 103Rh Signal Using Information Contained in 31P Spectrum of AA′XX′ 31P–103Rh Spin System,
Appl Magn Reson. 50 (2019) 563–568.
https://doi.org/10.1007/s00723-018-1083-1
B. Kharkov, X. Duan, E.S. Tovar, J.W. Canary, A. Jerschow,
Singlet excitation in the intermediate magnetic equivalence regime and field-dependent study of singlet-triplet leakage,
Phys Chem Chem Phys. 21 (2019) 2595–2600.
https://doi.org/10.1039/c8cp06883f
S.M.D.C. Perera, U. Chawla, U.R. Shrestha, D. Bhowmik, A.V. Struts, S. Qian, X.-Q. Chu, M.F. Brown,
Small-Angle Neutron Scattering Reveals Energy Landscape for Rhodopsin Photoactivation,
J Phys Chem Lett. 9 (2018) 7064–7071.
https://doi.org/10.1021/acs.jpclett.8b03048
K. Kämpf, S.A. Izmailov, S.O. Rabdano, A.T. Groves, I.S. Podkorytov, N.R. Skrynnikov,
What Drives 15N Spin Relaxation in Disordered Proteins? Combined NMR/MD Study of the H4 Histone Tail,
Biophys J. 115 (2018) 2348–2367.
https://doi.org/10.1016/j.bpj.2018.11.017
L. Jackalin, B.B. Kharkov, A.V. Komolkin, S.V. Dvinskikh,
Experimental strategies for 13C-15N dipolar NMR spectroscopy in liquid crystals at the natural isotopic abundance,
Phys Chem Chem Phys. 20 (2018) 22187–22196.
https://doi.org/10.1039/c8cp04161j
B. Kharkov, L. Strouk, T.E. Skinner, A. Jerschow,
Optimal control RF pulses for excitation and suppression of NMR signals in a conductive medium,
J Chem Phys. 149 (2018) 034201.
https://doi.org/10.1063/1.5031154
Yu.S. Varshavsky, T.G. Cherkasova, M.R. Galding, A.A. Korlyukov, I.S. Podkorytov, V.A. Gindin, S.N. Smirnov, A.S. Mazur, A.I. Rubaylo,
13C NMR spectrum of crystalline [Rh(Acac) (CO)2]: A contribution to the discussion on [Rh(Acac) (CO)2] molecular structure in the solid state,
Journal of Organometallic Chemistry. 874 (2018) 70–73.
https://doi.org/10.1016/j.jorganchem.2018.08.009
O.N. Rogacheva, S.A. Izmailov, L.V. Slipchenko, N.R. Skrynnikov,
A new structural arrangement in proteins involving lysine NH3+ group and carbonyl,
Sci Rep. 7 (2017) 16402.
https://doi.org/10.1038/s41598-017-16584-y
S.O. Rabdano, S.A. Izmailov, D.A. Luzik, A. Groves, I.S. Podkorytov, N.R. Skrynnikov,
Onset of disorder and protein aggregation due to oxidation-induced intermolecular disulfide bonds: case study of RRM2 domain from TDP-43,
Sci Rep. 7 (2017) 11161.
https://doi.org/10.1038/s41598-017-10574-w
S.A. Izmailov, I.S. Podkorytov, N.R. Skrynnikov,
Simple MD-based model for oxidative folding of peptides and proteins,
Sci Rep. 7 (2017) 9293.
https://doi.org/10.1038/s41598-017-09229-7
V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse, A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P. Schanda,
Slow conformational exchange and overall rocking motion in ubiquitin protein crystals,
Nat Commun. 8 (2017) 145.
https://doi.org/10.1038/s41467-017-00165-8
A.I. Solomatina, P.S. Chelushkin, D.V. Krupenya, I.S. Podkorytov, T.O. Artamonova, V.V. Sizov, A.S. Melnikov, V.V. Gurzhiy, E.I. Koshel, V.I. Shcheslavskiy, S.P. Tunik,
Coordination to Imidazole Ring Switches on Phosphorescence of Platinum Cyclometalated Complexes: The Route to Selective Labeling of Peptides and Proteins via Histidine Residues,
Bioconjug Chem. 28 (2017) 426–437.
https://doi.org/10.1021/acs.bioconjchem.6b00598
I.I. Tyuryaeva, O.G. Lyublinskaya, I.S. Podkorytov, N.R. Skrynnikov,
Origin of anti-tumor activity of the cysteine-containing GO peptides and further optimization of their cytotoxic properties,
Sci Rep. 7 (2017) 40217.
https://doi.org/10.1038/srep40217
T. Yuwen, Y. Xue, N.R. Skrynnikov,
Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos,
Biochemistry. 55 (2016) 1784–1800.
https://doi.org/10.1021/acs.biochem.5b01283
A.V. Struts, A.V. Barmasov, M.F. Brown,
Condensed-matter spectroscopy spectral methods for study of the g-protein-coupled receptor rhodopsin. II. Magnetic resonance methods,
Opt Spectrosc. 120 (2016) 286–293.
https://doi.org/10.1134/S0030400X16010197
S.O. Rabdano, A.V. Donets, M.A. Vovk, D. Michel, V.I. Chizhik,
“Hydration Shells” of CH2 Groups of ω-Amino Acids as Studied by Deuteron NMR Relaxation,
J Phys Chem B. 119 (2015) 13358–13366.
https://doi.org/10.1021/acs.jpcb.5b06584
B.T. Heaton, E.V. Grachova, S.P. Tunik, I.S. Podkorytov,
Comment on “The ligand polyhedral model approach to the mechanism of complete carbonyl exchange in [Rh4(CO)12] and [Rh6(CO)16]” by Brian F. G. Johnson, Dalton Transactions, 2015, 44, DOI: 10.1039/C4DT03360D,
Dalton Trans. 44 (2015) 16611–16613.
https://doi.org/10.1039/c5dt01099c
P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda,
Observing the overall rocking motion of a protein in a crystal,
Nat Commun. 6 (2015) 8361.
https://doi.org/10.1038/ncomms9361
A.V. Struts, A.V. Barmasov, M.F. Brown,
Spectral methods for study of the g-protein-coupled receptor rhodopsin. I. Vibrational and electronic spectroscopy,
Opt Spectrosc. 118 (2015) 711–717.
https://doi.org/10.1134/S0030400X15050240
A.V. Struts, U. Chawla, S.M.D.C. Perera, M.F. Brown,
Investigation of rhodopsin dynamics in its signaling state by solid-state deuterium NMR spectroscopy,
Methods Mol Biol. 1271 (2015) 133–158.
https://doi.org/10.1007/978-1-4939-2330-4_10
Y. Xue, T. Yuwen, F. Zhu, N.R. Skrynnikov,
Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos,
Biochemistry. 53 (2014) 6473–6495.
https://doi.org/10.1021/bi500904f
Yu.S. Varshavsky, M.R. Galding, V.N. Khrustalev, I.S. Podkorytov, S.N. Smirnov, V.A. Gindin, A.B. Nikolskii,
Rhodium(I) dimethyl sulfoxide oxyquinolinato carbonyl complex, [Rh(Oxq)(CO)(DMSO)]. NMR and X-ray structure data,
Journal of Organometallic Chemistry. 761 (2014) 123–126.
https://doi.org/10.1016/j.jorganchem.2014.03.019
T. Yuwen, N.R. Skrynnikov,
Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins,
J Magn Reson. 241 (2014) 155–169.
https://doi.org/10.1016/j.jmr.2013.08.008
Y. Xue, N.R. Skrynnikov,
Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics,
Protein Sci. 23 (2014) 488–507.
https://doi.org/10.1002/pro.2433
T. Yuwen, N.R. Skrynnikov,
CP-HISQC: a better version of HSQC experiment for intrinsically disordered proteins under physiological conditions,
J Biomol NMR. 58 (2014) 175–192.
https://doi.org/10.1007/s10858-014-9815-5