Research Articles      Review Articles      Commentaries     Perspective     Book Chapters

Research Articles

2018

[40] H. Yang, J. Perrier, P. C. Whitford^. Disorder guides domain rearrangment in EF-Tu. Proteins: Structure, Function, Bioinformatics. DOI:10.1002/prot.25575 manuscript

2017

[39] M. Levi, K. Nguyen, L. Dukaye, P. C. Whitford^. Quantifying the relationship between single-molecule probes and subunit rotation in the ribosome. Biophysical Journal, 113, 2777-2786, 2017. manuscript

[38] H. Yang, J. K. Noel, P. C. Whitford^. Anisotropic Fluctuations in the Ribosome Determine tRNA kinetics. Journal of Physical Chemistry B, 121, 10593-10601, 2017. manuscript

 

 

 

 

 

[37] P. Waduge, R. Hu, P. Bandarkar, H. Yamazaki, B. Cressiot, Q. Zhao, P. C Whitford^ and M. Wanunu^. Nanopore-based measurements of protein size, fluctuations, and conformational changes. ACS Nano, 11, 5706-5716, 2017. manuscript

[36] K. Nguyen, H. Yang, P. C. Whitford^. How the ribosomal A-site finger can lead to tRNA species-dependent dynamics. Journal of Physical Chemistry B, 121, 2767-2775, 2017. manuscript

2016

[35] J. K. Noel, P. C. Whitford^. How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome. Nature Communications. 7, 13314, 2016. manuscript

[34] K. Nguyen, P. C. Whitford^. Capturing transition states for tRNA hybrid-state formation in the ribosome. Journal of Physical Chemistry B. 120, 8768-8775, 2016. manuscript

[33] J. K. Noel^, M. Levi, M. Raghunathan, H. Lammert, R. L. Hayes, J. N. Onuchic^, P. C. Whitford^. SMOG 2: A versatile software package for generating structure-based models. PLOS Computational Biology. 12, e1004794, 2016. manuscript

[32] K. Nguyen, P. C. Whitford^. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nature Communications. 7, 10586, 2016. manuscript

2015

[31] R. Hayes, J. K. Noel, A. Mandic, P. C. Whitford, K. Y. Sanbonmatsu, U. Mohanty, J. N. Onuchic. Generalized manning condensation model captures the RNA ion atmosphere. Phys. Rev. Lett. 114, 258105, 2015.

[30] J. Jackson, K. Nguyen, P. C. Whitford^. Exploring the balance between folding and function in proteins and RNA. Int. J. Mol. Sci. 16, 6868-6889, 2015. manuscript

2014

[29] J. K. Noel, J. Chahine, V. B. P. Leite, P. C. Whitford^. Capturing transition paths and transition states for conformational rearrangements in the ribosome. Biophys. J. 107, 2881-2890, 2014. CORRECTION

[28] X. Lin, N. R. Eddy, J. K. Noel, P. C. Whitford, Q. Wang, J. Ma, J. N. Onuchic. Order and disorder control the functional rearrangement of influenza hemagglutinin. Proc. Nat. Acad. Sci. USA DOI: www.pnas.org/cgi/doi/10.1073/pnas.1412849111

[27] R. L. Hayes, J. K. Noel, P. C. Whitford, U. Mohanty, K. Y. Sanbonmatsu, J. N. Onuchic. Reduced model captures Mg2+-RNA interaction free energy of riboswitches. Biophysical Journal. 106, 1508, 2014.

2013

[26] P. C. Whitford^, S. C. Blanchard, J. H. D. Cate, K. Y. Sanbonmatsu. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comp. Biol. 9, e1003003, 2013.

[25] P. C. Whitford^, K. Y. Sanbonmatsu^. Simulating movement of tRNA motion through the ribosome during hybrid-state formation. J. Chem. Phys. 139, 121919, 2013.

2012 (Joined NEU faculty 9/12)

[24] J. Wang, R. J. Oliveira, X. Chu, P. C. Whitford, J. Chahine, W. Han, E. Wang, J. N. Onuchic, V. B. P. Leite. Topopgraphy of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proc. Nat. Acad. Sci. USA. 109, 15763-15768, 2012.

[23] R. L. Hayes, J. K. Noel, U. Mohanty, P. C. Whitford, S. P. Hennelly, J. N. Onuchic, K. Y. Sanbonmatsu. Magnesium fluctuations modulate RNA dynamics in the SAM-1 riboswitch. J. Amer. Chem. Soc. 134, 12043-12053, 2012.

[22] M. A. Jamros, L. C. deOliveira, P. C. Whitford, J. N. Onuchic, J. A. Adams, and P. A. Jennings. Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinast function. PLoS Comp. Biol. 8, e1002695, 2012.

[21] J. K. Noel, P. C. Whitford and J. N. Onuchic. The shadow method: A Generally-Applicable contact definition for capturing the dynamics of biomolecular folding and function. J. Phys. Chem. 116, 8692-8702, 2012.

[20] J. Singh, P. C. Whitford, N. Hayre, J. N. Onuchic and D. Cox.  Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways. Proteins: Struct. Func. Bioinfo. 80, 1299-1307, 2012.

[19] A. Ahmed, P. C. Whitford, K. Y. Sanbonmatsu and F. Tama.  Consensus between flexible fitting computational methods to interpret cryo-EM data. J. Struct. Biol. 177, 561-570, 2012.

2011

[18] P. C. Whitford, A. Ahmed, Y. Yu, S. P. Hennelly, F. Tama, C. M. T. Spahn, J. N. Onuchic and K. Y. Sanbonmatsu.  Excited states of ribosome translocation revealed through integrative molecular modeling.  Proc. Nat. Acad. Sci. USA. 108, 18943-18948, 2011.

[17] R. Nechushtai, H. Lammert, D. Michaeli, Y. Eizenberg-Domovish, J. A. Zuris, M. A. Luca, D. T. Capraro, A. Fish, O. Shimshon, M. Roy, A. Schug, P. C. Whitford, O. Livnah, J. N. Onuchic and P. A. Jennings.  Allostery in the ferredoxin protein motif does not involve a conformational switch.   Proc. Nat. Acad. Sci. USA.  108, 2240-2245, 2011.

2010

[16] P. C. Whitford^, J. N. Onuchic and K. Y. Sanbonmatsu. Connecting energy landscapes and experimental rates for aminoacyl-tRNA accommodation in the ribosome. J. Amer. Chem. Soc. 132, 13170-13171, 2010. (communication)

[15] A. H. Ratje, J. Loerke, A. Mikolajka, M. Brünner, P. W. Hildebrand, A. Starosta, A. Doenhoefer, S. R. Connell, P. Fucini, T. Mielke, P. C. Whitford, J. N. Onuchic, Y. Yanan, K. Y. Sanbonmatsu, R. K. Hartmann, P. A. Penczek, D. N. Wilson and C. M. T. Spahn.  Head swivel on the ribosome facilitates translocation via intra-subunit tRNA hybrid sites.  Nature 468, 713-716, 2010.

[14] M. A. Jamros, L. C. deOliveira, P. C. Whitford, J. N. Onuchic, J. A. Adams, D. K. Blumenthal and P. A. Jennings.  Proteins at work: A combined SAXS and theoretical determination of the multiple structures involved on the protein kinase functional landscape.  J. Biol. Chem. 285, 36121-36128, 2010.

[13] J. K. Noel, P. C. Whitford, K. Y. Sanbonmatsu, and J. N. Onuchic.  SMOG@ctbp: Simplified deployment of structure-based models in GROMACS. Nucleic Acid Research 38(suppl. 2), W657-W661, 2010.

[12] P. C. Whitford, P. Geggier, R. Altman, S. C. Blanchard, J. N. Onuchic, and K. Y. Sanbonmatsu.  Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.  RNA. 16, 1196-1204, 2010.

[11] R. J. Oliveira*, P. C. Whitford*^, J. Chahine, J. Wang, J. N. Onuchic, and V. B. P. Leite^. Exploring the origin of non-monotonic complex behavior and the effects of non-native interactions on the diffusive properties of protein folding. Biophys. J. 99, 600-608, 2010.

2009

[10] P. C. Whitford, A. Schug, J. Saunders, S. P. Hennelly, J. N. Onuchic, and K. Y. Sanbonmatsu. Nonlocal helix formation is key to understanding S-adenosylmethionine riboswitch function. Biophys. J. 96, L7-9, 2009.  (On cover).

[9] P. C. Whitford, J. K. Noel, S. Gosavi, A. Schug, K. Y. Sanbonmatsu, and J. N. Onuchic. An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields. Prot. Struct. Func. Bioinfo. 75, 430-441, 2009.

2008

[8] S. Gosavi, P. C. Whitford, P. A. Jennings, and J. N. Onuchic. Extracting function from a b-trefoil folding motif. Proc. Nat. Acad. Sci. 105, 10384–10389, 2008.

[7] P. C. Whitford, S. Gosavi, and J. N. Onuchic. Conformational transitions in adenylate kinase – Allosteric communication reduces misligation. J. Biol. Chem. 283, 2042–2048, 2008.

2007

[6] A. Schug, P. C. Whitford, Y. Levy, and J. N. Onuchic. Mutations as trapdoors to two competing native conformations of the rop-dimer. Proc. Nat. Acad. Sci. 104, 17674–17679, 2007.

[5] P. C. Whitford, O. Miyashita, Y. Levy, and J. N. Onuchic. Conformational transitions of adenylate kinase: Switching by cracking. J. Mol. Biol. 366, 1661–1671, 2007.

[4] J. E. Mills, P. C. Whitford, J. Shaffer, J. N. Onuchic, J. A. Adams, and P. A. Jennings. A novel disulfide bond in the SH2 domain of the C-terminal Src kinase controls catalytic activity. J. Mol. Biol. 365, 1460–1468, 2007.

2005

[3] P. C. Whitford, and G. D. J. Phillies. Enhanced septahedral ordering in cold  Lennard-Jones fluids. Phys. Rev. E 72, 021203, 2005.

[2] P. C. Whitford, and G. D. J. Phillies. Extended-range order, diverging static length scales, and local structure formation in cold Lennard-Jones fluids . J. Chem. Phys. 122, 044508, 2005.

2003

[1] G. D. J. Phillies, R. O’Connell, P. Whitford, and K. A. Streletzky. Mode structure of diffusive transport in hydroxypropylcellulose:water. J. Chem. Phys. 119, 9903–9913, 2003.

 

Review Articles

[5] P. C. Whitford. The ribosome’s energy landscape: Recent insights from computation. Biophys. Rev. 7, 301-310, 2015. DOI: 10.1007/s12551-014-0155-1

[4] P. C. Whitford^, J. N. Onuchic^. What protein folding teaches us about biological function and molecular machines. Curr. Opin. Struct. Biol. 30, 57-62, 2015.

[3] J. K. Noel, P. C. Whitford^. How simulations reveal dynamics, disorder and the energy landscapes of biomolecular function. Israel J. Chem. DOI: 10.1002/ijch.201400018, 2014.

[2] P. C. Whitford, K. Y. Sanbonmastu, J. N. Onuchic. Biomolecular dynamics: Order-disorder transitions and energy landscapes. Rep. Prog. Phys. 75, 076601, 2012.

[1] R. J. Oliveira, P. C. Whitford, J. Chahine, V. B. P. Leite and J. Wang.  Coordinate and time dependent diffusion dynamics in protein folding. Methods 52, 91-98, 2010.

 

Commentaries

[2] P. C. Whitford. Disorder guides protein function. Proc. Nat. Acad. Sci. USA. 110, 7114-7115, 2013.

[1] P. C. Whitford, J. N. Onuchic, and P. G. Wolynes. Energy landscape along an enzymatic reaction trajectory: hinges or cracks? HFSP J. 2, 61–64, 2008.

 

Perspective

[1] K. Nguyen, P. C. Whitford. Challenges in describing ribosome dynamics. Phys. Biol. 14, 023001, 2017. manuscript

 

Book Chapters

[3] K. Y. Sanbonmatsu, S. C. Blanchard and P. C. Whitford.  Molecular dynamics simulations of the ribosome. Biophysical approaches to translational control of gene expression. 2012. ISBN: 978-1-4614-3990-5

[2] P. C. Whitford, R. B. Altman, P. Geggier, D. Terry, J. B. Munro, J. N. Onuchic, C. M. T. Spahn, K. Y. Sanbonmatsu, S. C. Blanchard.  Chapter 24: Dynamic views of ribosome function: energy landscapes and ensembles.  The Ribosome: Structure, Function, and Dynamics.  2011. ISBN: 978-3-7091-0214-5.

[1] K. Y. Sanbonmatsu, S. C. Blanchard and P. C. Whitford. Chapter 4: Information processing by nanomachines: decoding by the ribosome. Molecular Machines. 2011. ISBN-13: 978-98143442