Publications

2019

1. I.K Sariyer, J. Gordon, T.H Burdo, H. Wollebo, E. Gianti, M. Donadoni, A. Bellizzi, S. Cicalese, R. Loomis, J.A. Robinson, V. Carnevale, J. Steiner, M.H. Ozdener, A.D. Miller, S. Amini, M.L. Klein, K. Khalili Suppression of Zika virus infection in brain by the antiretroviral drug, rilpivirine. Molecular Therapy 2019

2.  S.J. Black, A. Y. Ozdemir, E. Kashkina, T. Kent, T. Rusanov, D. Ristic, Y. Shin, A. Suma, T. Hoang, G. Chandramouly, L.A. Siddique, N. Borisonnik, K. Sullivan-Reed, J. S. Mallon, T. Skorski, V. Carnevale, K. S. Murakami, C. Wyman, R. T. Pomerantz. Molecular basis of microhomology-mediated end-joining by purified full-length Polθ. Nature Communications. 2019 Sep 27;10(1).

3.  M. A. Kasimova, T. Lynagh, Z. P. Sheikh, D. Granata, C. B. Borg, V. Carnevale, S. A. Pless. Evolutionarily conserved interactions within the pore domain of acid-sensing ion channels. Biophysical Journal (2019).

4. P. Scalia, G. Pandini, V. Carnevale, A. Giordano, S. J. Williams, Identification of a novel EphB4 phosphodegron regulated by the autocrine IGFII/IRA axis in malignant mesothelioma. Oncogene38(31), 5987-6001.

5. B. W. Roose, S. D. Zemerov, Y. Wang, M. A. Kasimova, V. Carnevale, I. J. Dmochowski A Structural Basis for 129Xe Hyper-CEST Signal in TEM-1 β-Lactamase ChemPhysChem, doi:10.1002/cphc.201800624

6.  R. Wang, M. DelloStritto, R. C. Remsing, V. Carnevale, M. L. Klein, and E. Borguet. Sodium Halide Adsorption and Water Structure at the α-Alumina (0001)/Water Interface The Journal of Physical Chemistry C (2019).

2018

7. M. Kasimova, A. Yazici, D. Granata, M. L. Klein, T. Rohacs, V. Carnevale A hypothetical molecular mechanism for TRPV1 activation that invokes rotation of an S6 asparagine, The Journal of General Physiology, 150(11), 1554-1566.

8. T. E. Hughes, R. A. Pumroy, A. T. Yazici, M. A. Kasimova, E. C. Fluck, K. W. Huynh, A. Samanta, S. Molugu, Z. H. Zhou, V. Carnevale, T. Rohacs V. Moiseenkova Bell. Structural insights on TRPV5 gating by endogenous modulators. 2018 Nature Communications, just accepted (bioRxiv 338798; doi: https://doi.org/10.1101/338798)

9. E. Yang, D. Granata, R. G. Eckenhoff, V. Carnevale, M. Covarrubias (2018). Propofol inhibits prokaryotic voltage-gated Na+ channels by promoting activation-coupled inactivation. The Journal of General Physiology, jgp-201711924.

10.   Y. Wang, E. Yang, M.M. Wells, V. Bondarenko, K. Woll, V. Carnevale, D. Granata, M.L. Klein, R. G. Eckenhoff, W.P. Dailey, M. Covarrubias, P. Tang, Y. Xu 2018. Propofol inhibits the voltage-gated sodium channel NaChBac at multiple sites. The Journal of General Physiology, pp.jgp-201811993.

11.   V. Carnevale 2018 Protonation underlies tonic vs. use-dependent block." Proceedings of the National Academy of Sciences USA 115.14: 3512-3514.

12.   M. Kasimova, A. Yazici, D. Granata, M. L. Klein, T. Rohacs, V. Carnevale 2018 Ion Channel Sensing: Are Fluctuations the Crux of the Matter? 2018 Journal of Physical Chemistry Letters, 9(6), 1260-1264.

13.   S. Molinarolo, S. Lee, L. Leisle, J.D. Lueck, D. Granata, V. Carnevale, C. A. Ahern 2018. Cross-kingdom auxiliary subunit modulation of a voltage-gated Sodium channel. Journal of Biological Chemistry, jbc-RA117.

14.   E. Gianti, V. Carnevale 2018 Computational Approaches to Studying Voltage-Gated Ion Channel Modulation by General Anesthetics in Chemical and Biochemical Approaches for the Study of Anesthetic Function, R. Eckenhoff and I Dmochowski Eds Methods in Enzymology vol. 602, pp. 25-59. Academic Press, 2018.

2017

15.   S. Molinarolo, D. Granata, V. Carnevale, and C.A. Ahern Mining Protein Evolution for Insights into Mechanisms of Voltage-Dependent Sodium Channel Auxiliary Subunits in Sodium Channels and Related Diseases in the Handbook of Experimental Pharmacology (HEP), ed. Mohammed Chahine, Springer Nature. 246 (2017): 33.

16.   R. J. Howard, V. Carnevale, L. Delemotte, U. A. Hellmich, and B. S. Rothberg. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport. Biochimica et biophysica acta (2017).

17.   Steinberg, Ximena, Marina A. Kasimova, Deny Cabezas-Bratesco, Jason D. Galpin, Ernesto Ladron-de-Guevara, Federica Villa, Vincenzo Carnevale, Leon Islas, Christopher A. Ahern, and Sebastian E. Brauchi. Conformational dynamics in TRPV1 channels reported by an encoded coumarin amino acid. eLife, 6, e28626

18.   K.A. Woll, K.A Skinner, E. Gianti, N.V. Bhanu, B.A. Garcia, V. Carnevale, R.G. Eckenhoff, and R. Gaudet, 2017. Sites Contributing to TRPA1 Activation by the Anesthetic Propofol Identified by Photoaffinity Labeling. Biophysical Journal113(10), pp.2168-2172.

19.   D. Granata, L. Ponzoni, C. Micheletti, V. Carnevale Patterns of coevolving amino acids unveil structural and dynamical domains, Proceedings of the National Academy of Sciences USA, 2017, 201712021

20.   A. M Razavi, L. Delemotte, J. R. Berlin, V. Carnevale, V. A. Voelz Molecular Simulations and Free energy calculations suggest a mechanism for Na,K-ATPase ion selectivity, Journal of Biological Chemistry (2017): jbc-M117.

21.   V. Carnevale, M. L Klein, Small molecule modulation of voltage gated sodium channels, Current Opinion in Structural Biology, Volume 43, April 2017, Pages 156-162, ISSN 0959-440X, http://dx.doi.org/10.1016/j.sbi.2017.02.002.

2016

22.   V. Carnevale, T. Rohacs TRPV1: a target for rational drug design Pharmaceuticals, 2016 9(3), 52

23.   S. C. van Keulen, E. Gianti, V. Carnevale, M. L. Klein, U. Rothlisberger, L. Delemotte Does proton conduction in the voltage-gated H+ channel hHv1 involve Grotthuss-like hopping via acidic residues? The Journal of Physical Chemistry B doi:10.1021/acs.jpcb.6b08339, 2016

24.   M. N. Kinde, V. Bondarenko D. Granata, W. Bu, P. Loll, V. Carnevale, M. L. Klein, R. G. Eckenhoff, P. Tang, Y. Xu 2016 19F NMR Quantification of Isoflurane Binding to the Voltage-Gated Sodium Channel NaChBac, Proceedings of the National Academy of Sciences USA, 113 (48) 13762-13767;

25.   E. Gianti, L. Delemotte, M. L. Klein, V. Carnevale On the Role of Water Density Fluctuations in the Inhibition of a Proton Channel, Proceedings of the National Academy of Sciences USA, 2016 113 (52) E8359-E8368;

26.   D. Granata and V. Carnevale. Accurate Estimation of the Intrinsic Dimension Using Graph Distances: Unraveling the Geometric Complexity of Datasets, Scientific Reports, 6, 2016.

27.   Y. Wang, B. W. Roose, E. J. Palovcak, V. Carnevale, I. J. Dmochowski A Genetically Encoded β-Lactamase Reporter for Ultrasensitive 129Xe NMR in Mammalian Cells Angewandte Chemie DOI: 10.1002/anie.201604055, 2016

28.    P. Velisetty, I. Borbiro, M. A. Kasimova, L. Liu, D. Badheka, V. Carnevale, T. Rohacs A molecular determinant of phosphoinositide affinity in mammalian TRPV channels Scientific Reports 6: 27652, 2016

29.   K. Elokely, P. Velisetty, L. Delemotte, E. Palovcak, M.L. Klein, T. Rohacs, V. Carnevale Understanding TRPV1 Activation by Ligands: Insights from the Binding Modes of Capsaicin and Resiniferatoxin PNAS, doi: 10.1073/pnas.1517288113, 2016

30.   M. A. Kasimova, D. Granata, V. Carnevale Voltage-Gated Sodium Channels: Evolutionary History and Distinctive Sequence Features In Sergei Noskov, Sidney Simon, Robert French editors, Sodium Channels Across Phyla and Functions Current Topics in Membranes, Volume 78, 2016

2015

31.   S.M. Mohamed, K.M. Elokely, E.Y. Bachkeet, S.A. Bayoumib, V. Carnevale, M.L. Klein, S.J. Cutler, S.A. Ross New Glycosides and Trypanocidal Metabolites from Vangueria edulis. Natural Product Communications 10(11):1897-900, 2015.

32.   M. Covarrubias, A. F Barber, V. Carnevale, W. Treptow, and R. G Eckenhoff. Mechanistic insights into the modulation of voltage-gated ion channels by inhaled anesthetics. BIOPHYSICAL JOURNAL, 109:10, 2003-2011, 2015.

33.   L. Ponzoni, G. Polles, V. Carnevale, and C. Micheletti. SPECTRUS: a dimensionality reduction approach for identifying dynamical domains in protein complexes from limited structural datasets. Structure, 23:8, 1516-1525, 2015

34.   A. W. Nicholson, S. K. Redhu, A. Stopar, L. Coral, V. Carnevale, and M. Castronovo. Emergent properties and functions of nanoconfined nucleic acid architectures. In Volker Erdmann, Stefan Jurga, and Jan Barciszewski, editors, RNA and DNA Diagnostics, RNA Technologies. Springer New York, 2015.

35.   E. Palovcak, L. Delemotte, M. Klein, and V. Carnevale. Comparative sequence analysis suggests a conserved gating mechanism for TRP channels. JOURNAL OF GENERAL PHYSIOLOGY, 2015, DOI:10.1085/jgp.201411329

36.   L. Delemotte, M. A. Kasimova, M. L. Klein, M. Tarek, V. Carnevale Free Energy Landscape of Ion-Channel Voltage-Sensor-Domain Activation PROC. NATL. ACAD. SCI. USA, doi: 10.1073/pnas.1416959112

37.   S. Paudyal, M. Alfonso-Prieto, V. Carnevale, S. Redhu,  M. L. Klein, A. W. Nicholson Combined Computational and Experimental Analysis of a Complex of Ribonuclease III and the Regulatory Macrodomain Protein, YmdB PROTEINS: Structure, Function, and Bioinformatics, doi:10.1002/prot.24751

2014

38.   E. Gianti, V. Carnevale, W.F. Degrado, M.L. Klein, G. Fiorin Hydrogen-bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-based Inhibitors , JOURNAL OF PHYSICAL CHEMISTRY B, doi:10.1021/jp506807y

39.   A. Bankura, A. Karmakar, V. Carnevale, A Chandra, M.L. Klein Structure, Dynamics, and Spectral Diffusion of Water from First-Principles Molecular Dynamics, JOURNAL OF PHYSICAL CHEMISTRY C, doi:10.1021/jp506120t

40.   S. Dewan, V. Carnevale, A. Bankura, A. Eftekhari-Bafrooei, G. Fiorin, M. L. Klein, E. Borguet. Structure of Water at Charged Interfaces: A Molecular Dynamics Study. LANGMUIR, 2014, 30 (27), pp 8056–8065, doi:10.1021/la5011055

41.   A. F. Barber, V. Carnevale, M. L. Klein, R. G. Eckenhoff, M. Covarrubias Modulation of a voltage-gated Na+ channel by sevoflurane involves multiple sites and distinct mechanisms. PROC. NATL. ACAD. SCI. USA, doi: 10.1073/pnas.1405768111.

42.   A. Bankura, V. Carnevale, M. L. Klein Hydration structure of Na+ and K+ from ab initio molecular dynamics based on modern density functional theory. MOLECULAR PHYSICS, doi: 10.1080/00268976.2014.905721

43.   E. Palovcak, L. Delemotte, M.L. Klein, V. Carnevale Evolutionary imprint of activation: The design principles of VSDs THE JOURNAL OF GENERAL PHYSIOLOGY 143 (2), 145-156.

44.   V. C. Quy*, V. Carnevale*, L. Manganaro, M. Lusic, G. Rossetti, V. Leone, C. Fenollar-Ferrer, S. Raugei, G. Del Sal, M. Giacca, P. Carloni. HIV-1 Integrase Binding to its Cellular Partners: A Perspective from Computational Biology. (* - equally contributing authors) CURRENT PHARMACEUTHICAL DESIGN, Sep 2. 2014

2013

45.   H. Dong, G. Fiorin, V. Carnevale, W. Treptow, M. L. Klein Pore waters regulate ion permeation in a calcium release-activated calcium channel PROC. NATL. ACAD. SCI. USA 110(43), 17332-17337 (2013).

46.   A. Ma*, G. Fiorin*, V. Carnevale*, R. A. Lamb, M. L. Klein, W. F. DeGrado, L. H. Pinto Asp44 Stabilizes the Trp41 Gate of the M2 Proton Channel of Influenza A Virus STRUCTURE 21(11), 2033-2041 (2013) (* - equally contributing authors).

47.   S. G. Raju, A. B. Barber, D. LeBard, M. L. Klein, V. Carnevale Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation PLOS COMPUTATIONAL BIOLOGY doi:10.1371/journal.pcbi.1003090 (2013).

48.   A. Bankura, M. L. Klein, V. Carnevale Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics. CHEMICAL PHYSICS – doi: 10.1016/j.chemphys.2013.03.006.

49.   L. Stock, L. Delemotte, V. Carnevale, W. Treptow, M. L. Klein Conduction in a biological sodium channel JOURNAL OF PHYSICAL CHEMISTRY B 117(14), 3782–3789 (2013).

50.   A. Bankura, V. Carnevale, M. L. Klein Hydration structure of salt solutions from ab initio molecular dynamics JOURNAL OF CHEMICAL PHYSICS 138, 014501 (2013).

2012

51.   C. Amaral, V. Carnevale, M. L. Klein, W. Treptow Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations PROC. NATL. ACAD SCI. USA 109(52), 21336-21341 (2012).

52.   A. F. Barber*, V. Carnevale*, S.G. Raju*, C. Amaral, Werner Treptow, M. L. Klein Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOMEMBRANES, 1818(9), 2120-2125 (2012)(* - equally contributing authors).

53.   C. Fenollar-Ferrer, C. Anselmi, V. Carnevale, S. Raugei, P. Carloni Insights on the acetylated NF-κB transcription factor complex with DNA from molecular dynamics simulations. PROTEINS, 80, 1560–1568 (2012)

54.   V. Caracciolo, G. Laurenti, G. Romano, V. Carnevale, A. M. Cimini, C. Crozier-Fitzgerald, E. Gentile, G. Russo, A. Giordano Flavopiridol induces phosphorylation of AKT in a human glioblastoma cell line, in contrast to siRNA-mediated silencing of Cdk9: Implications for drug design and development. CELL CYCLE, 11(6), 1202-1216 (2012)

2011

55.   V. Carnevale, W. Treptow, M.L. Klein Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations. JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2(19), 2504–2508 (2011)

56.   J. Wang, C. Ma, G. Fiorin, V. Carnevale, T. Wang, F. Hu, R.A. Lamb, L.H. Pinto, M. Hong, M.L. Klein, W.F. Degrado Molecular Dynamics Simulation Directed Rational Design of Inhibitors Targeting Drug-Resistant Mutants of Influenza A Virus M2. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133(32), 12834–12841 (2011)

2010

57.   J.E. Donald, Y. Zhang, G. Fiorin, V. Carnevale, D. R. Slochower, F. Gai, M.L. Klein, W.F. DeGrado Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion. PROC. NATL. ACAD SCI. USA 108(10), 3958-63 (2010)

58.   V. Carnevale, C. Micheletti, F. Pontiggia and R. Potestio Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins. In A. Kolinski editor, Multiscale Approaches to Protein Modeling, Springer Verlag, 2010.

59.   G. Fiorin, V. Carnevale, W. F. DeGrado. The Flu's Proton Escort. SCIENCE 330, 456-458 (2010)

60.   V. Carnevale, G. Fiorin, B. G. Levine, W. F. DeGrado, M. L. Klein. Multiple proton confinement in the M2 channel from the influenza A virus. JOURNAL OF PHYSICAL CHEMISTRY C 114(48):20856-20863 (2010)

61.   R. Acharya*, V. Carnevale*, G. Fiorin*, B. G. Levine*, A. L. Polishchuk*, V. Balannik, I. Samish, R. A. Lamb, L. H. Pinto, W. F. DeGrado, M. L. Klein. Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. PROC. NATL. ACAD. SCI. USA 107, 15075-15080 (2010) (* - equally contributing authors).

62.   V. Balannik, V. Carnevale, G. Fiorin, B. G. Levine, R. A. Lamb, M. L. Klein, W. F. Degrado, L. H. Pinto. Functional studies and modeling of pore-lining residue mutants of the influenza A virus M2 ion channel. BIOCHEMISTRY 49(4), 696-708 (2010)

2009

63.   V. Carnevale, S. Raugei. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation. JOURNAL OF CHEMICAL PHYSICS 131(22), 225103-225103 (2009)

64.   V. Carnevale, S. Raugei, M. Neri, S. Pantano, C. Micheletti, and P. Carloni. Multi-scale modeling of HIV-1 proteins. JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 898, 97 (2009).

2008

65.   C. Fenollar Ferrer*, V. Carnevale*, S. Raugei, and P. Carloni. HIV-1 integrase-DNA interactions investigated by molecular modelling. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 9, 231 (2008). (* - equally contributing authors)

66.   V. Carnevale, S. Raugei, S. Piana, and P. Carloni. On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study. COMPUTER PHYSICS COMMUNICATIONS 179, 120 (2008).

67.   A. Zen, V. Carnevale, A. M. Lesk, and C. Micheletti. Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families. PROTEIN SCIENCE 17, 918 (2008).

68.   M. Neri, M. Baaden, V. Carnevale, C. Anselmi, A. Maritan, and P. Carloni. Microseconds dynamics simulations of the outer-membrane protease T. BIOPHYSICAL JOURNAL 94, 71 (2008).

2007

69.   V. Carnevale, S. Raugei, C. Micheletti, and P. Carloni. Large-scale motions and electrostatic properties of furin and HIV-1 protease. JOURNAL OF PHYSICAL CHEMISTRY A 111, 12327 (2007).

70.   V. Carnevale, F. Pontiggia, and C. Micheletti. Structural and dynamical alignment of enzymes with partial structural similarity. JOURNAL OF PHYSICS-CONDENSED MATTER 19 (2007).

2006

71.   V. Carnevale, S. Raugei, C. Micheletti, and P. Carloni. Convergent dynamics in the protease enzymatic superfamily. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 128, 9766 (2006).

72.   M. Neri, C. Anselmi, V. Carnevale, A. Vargiu, and P. Carloni. Molecular dynamics simulations of outer-membrane protease T from E-coli based on a hybrid coarse-grained/atomistic potential, JOURNAL OF PHYSICS-CONDENSED MATTER 18, S347 (2006).

2003

73.   R. Asgari, M. Polini, V. Carnevale, and M. Tosi. Vibrational excitations in the paired phases of a two-dimensional electron crystal in a perpendicular magnetic field. PHYSICA B-CONDENSED MATTER 336, 387 (2003).