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Alan M. Grossfield, Ph.D.


Showing all 62 journal articles & 0 books available

Journal Articles

Getsy PM, Young AP, Bates JN, Baby SM, Seckler JM, Grossfield A, Hsieh YH, Lewis THJ, Jenkins MW, Gaston B, Lewis SJ. "S-nitroso-L-cysteine stereoselectively blunts the adverse effects of morphine on breathing and arterial blood gas chemistry while promoting analgesia." Biomedicine & pharmacotherapy = Biomédecine & pharmacothérapie.. 2022 Sep; 153:113436. Epub 2022 Jul 26.

Seckler JM, Robinson EN, Lewis SJ, Grossfield A. "Surveying non-visual arrestins reveals allosteric interactions between functional sites." Proteins.. 2022 Aug 21; Epub 2022 Aug 21.

Onukwufor JO, Farooqi MA, Vodi?ková A, Koren SA, Baldzizhar A, Berry BJ, Beutner G, Porter GA, Belousov V, Grossfield A, Wojtovich AP. "A reversible mitochondrial complex I thiol switch mediates hypoxic avoidance behavior in C. elegans." Nature communications.. 2022 May 3; 13(1):2403. Epub 2022 May 03.

Getsy PM, Young AP, Grossfield A, Seckler JM, Wilson CG, Gaston B, Bates JN, Lewis SJ. "D-Cysteine ethylester and D-cystine dimethylester reverse the deleterious effects of morphine on arterial blood-gas chemistry and Alveolar-arterial gradient in anesthetized rats." Respiratory physiology & neurobiology.. 2022 Apr 18; :103912. Epub 2022 Apr 18.

Sur S, Grossfield A. "Effects of Cholesterol on the mechanism of fengycin, a biofungicide." Biophysical journal.. 2022 Apr 14; Epub 2022 Apr 14.

Getsy PM, Baby SM, Gruber RB, Gaston B, Lewis THJ, Grossfield A, Seckler JM, Hsieh YH, Bates JN, Lewis SJ. "S-Nitroso-L-Cysteine Stereoselectively Blunts the Deleterious Effects of Fentanyl on Breathing While Augmenting Antinociception in Freely-Moving Rats." Frontiers in pharmacology.. 2022 13:892307. Epub 2022 May 26.

Seckler JM, Grossfield A, May WJ, Getsy PM, Lewis SJ. "Nitrosyl factors play a vital role in the ventilatory depressant effects of fentanyl in unanesthetized rats." Biomedicine & pharmacotherapy = Biomédecine & pharmacothérapie.. 2021 Dec 22; 146:112571. Epub 2021 Dec 22.

Gaston B, Baby SM, May WJ, Young AP, Grossfield A, Bates JN, Seckler JM, Wilson CG, Lewis SJ. "D-Cystine di(m)ethyl ester reverses the deleterious effects of morphine on ventilation and arterial blood gas chemistry while promoting antinociception." Scientific reports.. 2021 May 11; 11(1):10038. Epub 2021 May 11.

Grossfield A. "How To Be a Good Member of a Scientific Software Community [Article v1.0]." Living journal of computational molecular science.. 2021 3(1)

Romo TD, Grossfield A, Markelz AG. "Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis." Journal of chemical information and modeling.. 2020 Oct 26; Epub 2020 Oct 26.

Maji D, Grossfield AM, Kielkopf CL. "Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery." Biochimica et biophysica acta. Gene regulatory mechanisms.. 2019 Nov 7; :194440. Epub 2019 Nov 07.

Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH. "Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations." Journal of chemical theory and computation.. 2018 Nov 27; Epub 2018 Nov 27.

Thompson JL, Lai-Zhao Y, Stathopulos PB, Grossfield A, Shuttleworth TJ. "Phosphorylation-mediated structural changes within the SOAR domain of stromal interaction molecule 1 enable specific activation of distinct Orai channels." The Journal of biological chemistry.. 2018 Jul 13; 293(28):11241.

Thompson JL, Zhao Y, Stathopulos PB, Grossfield A, Shuttleworth TJ. "Phosphorylation-mediated structural changes within the SOAR domain of stromal interaction molecule 1 enable specific activation of distinct Orai channels." The Journal of biological chemistry.. 2018 Mar 2; 293(9):3145-3155. Epub 2018 Jan 11.

Sur S, Romo TD, Grossfield A. "Selectivity and Mechanism of Fengycin, an Antimicrobial Lipopeptide, from Molecular Dynamics." The journal of physical chemistry. B. 2018 Mar 1; 122(8):2219-2226. Epub 2018 Feb 15.

Salas-Estrada LA, Leioatts N, Romo TD, Grossfield A. "Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions." Biophysical journal.. 2018 Jan 23; 114(2):355-367.

Grossfield A, Patrone PN, Roe DR, Schultz AJ, Siderius DW, Zuckerman DM. "Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]." Living journal of computational molecular science.. 2018 1(1)Epub 2018 Oct 27.

Romo TD, Lewis AK, Braun AR, Grossfield A, Sachs JN. "Minimal Nucleation State of ?-Synuclein Is Stabilized by Dynamic Threonine-Water Networks." ACS chemical neuroscience.. 2017 Sep 20; 8(9):1859-1864. Epub 2017 Jul 10.

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH. "Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics." Journal of chemical theory and computation.. 2017 Feb 14; 13(2):900-915. Epub 2017 Jan 24.

Lin D, Grossfield A. "Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity." Biophysical journal.. 2015 Aug 18; 109(4):750-9.

Leioatts N, Romo TD, Danial SA, Grossfield A. "Retinal Conformation Changes Rhodopsin's Dynamic Ensemble." Biophysical journal.. 2015 Aug 4; 109(3):608-17.

Romo TD, Leioatts N, Grossfield A. "Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations." Journal of computational chemistry.. 2014 Dec 15; 35(32):2305-18. Epub 2014 Oct 18.

Lin D, Grossfield A. "Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity." Biophysical journal.. 2014 Oct 21; 107(8):1862-1872.

Leioatts N, Suresh P, Romo TD, Grossfield A. "Structure-based simulations reveal concerted dynamics of GPCR activation." Proteins.. 2014 Oct; 82(10):2538-51. Epub 2014 Jun 09.

Mnpotra JS, Qiao Z, Cai J, Lynch DL, Grossfield A, Leioatts N, Hurst DP, Pitman MC, Song ZH, Reggio PH. "Structural basis of G protein-coupled receptor-Gi protein interaction: formation of the cannabinoid CB2 receptor-Gi protein complex." The Journal of biological chemistry.. 2014 Jul 18; 289(29):20259-72. Epub 2014 May 22.

Romo TD, Grossfield A. "How fast is your camera? Timescales for molecular motion and their role in restraining molecular dynamics." Biophysical journal.. 2014 Jun 17; 106(12):2549-51.

Romo TD, Grossfield A. "Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations." Biophysical journal.. 2014 Apr 15; 106(8):1553-4.

Kimura T, Vukoti K, Lynch DL, Hurst DP, Grossfield A, Pitman MC, Reggio PH, Yeliseev AA, Gawrisch K. "Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations." Proteins.. 2014 Mar; 82(3):452-65. Epub 2013 Oct 17.

Leioatts N, Mertz B, Martinez-Mayorga K, Romo TD, Pitman MC, Feller SE, Grossfield A, Brown MF. "Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures." Biochemistry.. 2014 Jan 21; 53(2):376-85. Epub 2014 Jan 08.

Horn JN, Kao TC, Grossfield A. "Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin." Advances in experimental medicine and biology.. 2014 796:75-94.

Horn JN, Cravens A, Grossfield A. "Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics." Biophysical journal.. 2013 Oct 1; 105(7):1612-23.

Seckler JM, Leioatts N, Miao H, Grossfield A. "The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures." Proteins.. 2013 Oct; 81(10):1792-801. Epub 2013 Aug 16.

Horn JN, Romo TD, Grossfield A. "Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics." Biochemistry.. 2013 Aug 20; 52(33):5604-10. Epub 2013 Aug 09.

Grossfield A. "Special issue on lipid-protein interactions." Chemistry and physics of lipids.. 2013 Apr; 169:1.

Leioatts N, Romo TD, Grossfield A. "Elastic Network Models are Robust to Variations in Formalism." Journal of chemical theory and computation.. 2012 Jul 10; 8(7):2424-2434. Epub 2012 Jun 05.

Olausson BE, Grossfield A, Pitman MC, Brown MF, Feller SE, Vogel A. "Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes." Journal of the American Chemical Society.. 2012 Mar 7; 134(9):4324-31. Epub 2012 Feb 22.

Horn JN, Sengillo JD, Lin D, Romo TD, Grossfield A. "Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics." Biochimica et biophysica acta.. 2012 Feb; 1818(2):212-8. Epub 2011 Jul 28.

Romo TD, Grossfield A. "Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation." Journal of chemical theory and computation.. 2011 Aug 9; 7(8):2464-72. Epub 2011 Jul 01.

Romo TD, Bradney LA, Greathouse DV, Grossfield A. "Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations." Biochimica et biophysica acta.. 2011 Aug; 1808(8):2019-30. Epub 2011 Apr 06.

Grossfield A. "Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations." Biochimica et biophysica acta.. 2011 Jul; 1808(7):1868-78. Epub 2011 Apr 03.

Romo TD, Grossfield A. "Validating and improving elastic network models with molecular dynamics simulations." Proteins.. 2011 Jan; 79(1):23-34. Epub 2010 Sep 24.

Hurst DP, Grossfield A, Lynch DL, Feller S, Romo TD, Gawrisch K, Pitman MC, Reggio PH. "A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor." The Journal of biological chemistry.. 2010 Jun 4; 285(23):17954-64. Epub 2010 Mar 10.

Romo TD, Grossfield A, Pitman MC. "Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics." Biophysical journal.. 2010 Jan 6; 98(1):76-84.

Khelashvili G, Grossfield A, Feller SE, Pitman MC, Weinstein H. "Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations." Proteins.. 2009 Aug 1; 76(2):403-17.

Grossfield A, Zuckerman DM. "Quantifying uncertainty and sampling quality in biomolecular simulations." Annual reports in computational chemistry. 2009 Jan 1; 5:23-48.

Romo TD, Grossfield A. "LOOS: an extensible platform for the structural analysis of simulations." Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society.. 2009 2009:2332-5.

Grossfield A, Pitman MC, Feller SE, Soubias O, Gawrisch K. "Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin." Journal of molecular biology.. 2008 Aug 29; 381(2):478-86. Epub 2008 May 22.

O'Neil LL, Grossfield A, Wiest O. "Base flipping of the thymine dimer in duplex DNA." The journal of physical chemistry. B. 2007 Oct 11; 111(40):11843-9. Epub 2007 Sep 15.

Lau PW, Grossfield A, Feller SE, Pitman MC, Brown MF. "Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations." Journal of molecular biology.. 2007 Sep 28; 372(4):906-17. Epub 2007 Jun 26.

Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. "Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers." Biophysical journal.. 2007 Jun 1; 92(11):3817-29. Epub 2007 Mar 09.

Grossfield A, Feller SE, Pitman MC. "Convergence of molecular dynamics simulations of membrane proteins." Proteins.. 2007 Apr 1; 67(1):31-40.

Martínez-Mayorga K, Pitman MC, Grossfield A, Feller SE, Brown MF. "Retinal counterion switch mechanism in vision evaluated by molecular simulations." Journal of the American Chemical Society.. 2006 Dec 27; 128(51):16502-3.

Jiao D, King C, Grossfield A, Darden TA, Ren P. "Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential." The journal of physical chemistry. B. 2006 Sep 21; 110(37):18553-9.

Grossfield A, Feller SE, Pitman MC. "Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation." The journal of physical chemistry. B. 2006 May 11; 110(18):8907-9.

Grossfield A, Feller SE, Pitman MC. "A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids." Proceedings of the National Academy of Sciences of the United States of America.. 2006 Mar 28; 103(13):4888-93. Epub 2006 Mar 17.

Pitman MC, Grossfield A, Suits F, Feller SE. "Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment." Journal of the American Chemical Society.. 2005 Apr 6; 127(13):4576-7.

Grossfield A. "Dependence of ion hydration on the sign of the ion's charge." The Journal of chemical physics.. 2005 Jan 8; 122(2):024506.

Drozdov AN, Grossfield A, Pappu RV. "Role of solvent in determining conformational preferences of alanine dipeptide in water." Journal of the American Chemical Society.. 2004 Mar 3; 126(8):2574-81.

Grossfield A, Ren P, Ponder JW. "Ion solvation thermodynamics from simulation with a polarizable force field." Journal of the American Chemical Society.. 2003 Dec 17; 125(50):15671-82.

Grossfield A, Sachs J, Woolf TB. "Dipole lattice membrane model for protein calculations." Proteins.. 2000 Nov 1; 41(2):211-23.

Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB. "Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations." Journal of molecular biology.. 2000 Sep 22; 302(3):727-46.

Woolf TB, Grossfield A, Tychko M. "Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations." Biophysical journal.. 2000 Feb; 78(2):608-25.