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Alan M. Grossfield, Ph.D.

Alan M. Grossfield, Ph.D.

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About Me

Faculty Appointments

Associate Professor - Department of Biochemistry and Biophysics (SMD)

Research

My research interests revolve around the use of computer modeling to understand the structure and thermodynamics of biological molecules. In particular, I am most interested in understanding the biology and physics of lipid-protein interactions. These interactions underlie a fantastic array of biolo...
My research interests revolve around the use of computer modeling to understand the structure and thermodynamics of biological molecules. In particular, I am most interested in understanding the biology and physics of lipid-protein interactions. These interactions underlie a fantastic array of biological processes, including cell-signaling by GPCRs and some immune reactions, specifically the action of antimicrobial peptides.

Publications

Journal Articles

System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers.

Poruthoor AJ, Stallone JJ, Miaro M, Sharma A, Grossfield A

The Journal of chemical physics.. 2024 October 14161 (14)Epub 1900 01 01.

Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics.

Poruthoor AJ, Sharma A, Grossfield A

Biophysical journal.. 2023 November 7122 (21):4144-4159. Epub 09/23/2023.

Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.

Poruthoor AJ, Grossfield A

bioRxiv : the preprint server for biology.. 2023 August 28 Epub 08/28/2023.

Ionizable Amino Lipids Distribution and Effects on DSPC/Cholesterol Membranes: Implications for Lipid Nanoparticle Structure.

Dehghani-Ghahnaviyeh S, Smith M, Xia Y, Dousis A, Grossfield A, Sur S

The journal of physical chemistry. B. 2023 August 10127 (31):6928-6939. Epub 07/27/2023.

Application of molecular dynamics to elucidate key binding interactions for the development of therapeutics against opioid overdose.

Robinson EN, Grossfield A

Biophysical journal.. 2023 February 10122 (3S1):183a. Epub 1900 01 01.

X-ray scattering exhibits time-resolved view of rhodopsin activation.

Menon CSK, Karpos K, Grant TD, Struts AV, Fried SDE, Perera SMDC, Kosheleva IV, Salas-Estrada L, Grossfield A, Fromme P, Kirian RA, Brown MF

Biophysical journal.. 2023 February 10122 (3S1):191a. Epub 1900 01 01.

Femtosecond dynamics of rhodopsin revealed by X-ray laser.

Brown MF, Grant TD, Perera SMDC, Salas-Estrada L, Struts AV, Karpos K, Chawla U, Fried SDE, Menon CSK, Weerasinghe N, Meza D, Mendez D, Grossfield A, Fromme P, Kirian RA

Biophysical journal.. 2023 February 10122 (3S1):199a. Epub 1900 01 01.

LOOS: A suite of tools for analyzing molecular dynamics simulations.

Grossfield A, Romo TD

Biophysical journal.. 2023 February 10122 (3S1):425a. Epub 1900 01 01.

Accurate estimation of free energy landscape of phase separation in lipid bilayers.

James Poruthoor A, Grossfield A

Biophysical journal.. 2023 February 10122 (3S1):85a-86a. Epub 1900 01 01.

Surveying nonvisual arrestins reveals allosteric interactions between functional sites.

Seckler JM, Robinson EN, Lewis SJ, Grossfield A

Proteins.. 2023 January 91 (1):99-107. Epub 08/27/2022.

S-nitroso-L-cysteine stereoselectively blunts the adverse effects of morphine on breathing and arterial blood gas chemistry while promoting analgesia.

Getsy PM, Young AP, Bates JN, Baby SM, Seckler JM, Grossfield A, Hsieh YH, Lewis THJ, Jenkins MW, Gaston B, Lewis SJ

Biomedicine & pharmacotherapy = Biomédecine & pharmacothérapie.. 2022 September 153 :113436. Epub 07/26/2022.

D-cysteine ethyl ester and D-cystine dimethyl ester reverse the deleterious effects of morphine on arterial blood-gas chemistry and Alveolar-arterial gradient in anesthetized rats.

Getsy PM, Young AP, Grossfield A, Seckler JM, Wilson CG, Gaston B, Bates JN, Lewis SJ

Respiratory physiology & neurobiology.. 2022 August 302 :103912. Epub 04/18/2022.

Effects of cholesterol on the mechanism of fengycin, a biofungicide.

Sur S, Grossfield A

Biophysical journal.. 2022 May 17121 (10):1963-1974. Epub 04/14/2022.

A reversible mitochondrial complex I thiol switch mediates hypoxic avoidance behavior in C. elegans.

Onukwufor JO, Farooqi MA, Vodi?ková A, Koren SA, Baldzizhar A, Berry BJ, Beutner G, Porter GA, Belousov V, Grossfield A, Wojtovich AP

Nature communications.. 2022 May 313 (1):2403. Epub 05/03/2022.

Nitrosyl factors play a vital role in the ventilatory depressant effects of fentanyl in unanesthetized rats.

Seckler JM, Grossfield A, May WJ, Getsy PM, Lewis SJ

Biomedicine & pharmacotherapy = Biomédecine & pharmacothérapie.. 2022 February 146 :112571. Epub 12/22/2021.

S-Nitroso-L-Cysteine Stereoselectively Blunts the Deleterious Effects of Fentanyl on Breathing While Augmenting Antinociception in Freely-Moving Rats.

Getsy PM, Baby SM, Gruber RB, Gaston B, Lewis THJ, Grossfield A, Seckler JM, Hsieh YH, Bates JN, Lewis SJ

Frontiers in pharmacology.. 2022 13 :892307. Epub 05/26/2022.

D-Cystine di(m)ethyl ester reverses the deleterious effects of morphine on ventilation and arterial blood gas chemistry while promoting antinociception.

Gaston B, Baby SM, May WJ, Young AP, Grossfield A, Bates JN, Seckler JM, Wilson CG, Lewis SJ

Scientific reports.. 2021 May 1111 (1):10038. Epub 05/11/2021.

How To Be a Good Member of a Scientific Software Community [Article v1.0].

Grossfield A

Living journal of computational molecular science.. 2021 3 (1)Epub 1900 01 01.

Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis.

Romo TD, Grossfield A, Markelz AG

Journal of chemical information and modeling.. 2020 December 2860 (12):6419-6426. Epub 10/26/2020.

Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery.

Maji D, Grossfield AM, Kielkopf CL

Biochimica et biophysica acta. Gene regulatory mechanisms.. 2019 1862 (11-12):194440. Epub 11/09/2019.

Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.

Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH

Journal of chemical theory and computation.. 2018 December 1114 (12):6598-6612. Epub 11/27/2018.

Phosphorylation-mediated structural changes within the SOAR domain of stromal interaction molecule 1 enable specific activation of distinct Orai channels.

Thompson JL, Lai-Zhao Y, Stathopulos PB, Grossfield A, Shuttleworth TJ

The Journal of biological chemistry.. 2018 July 13293 (28):11241. Epub 1900 01 01.

Phosphorylation-mediated structural changes within the SOAR domain of stromal interaction molecule 1 enable specific activation of distinct Orai channels.

Thompson JL, Zhao Y, Stathopulos PB, Grossfield A, Shuttleworth TJ

The Journal of biological chemistry.. 2018 March 2293 (9):3145-3155. Epub 01/11/2018.

Selectivity and Mechanism of Fengycin, an Antimicrobial Lipopeptide, from Molecular Dynamics.

Sur S, Romo TD, Grossfield A

The journal of physical chemistry. B. 2018 March 1122 (8):2219-2226. Epub 02/15/2018.

Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions.

Salas-Estrada LA, Leioatts N, Romo TD, Grossfield A

Biophysical journal.. 2018 January 23114 (2):355-367. Epub 1900 01 01.

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0].

Grossfield A, Patrone PN, Roe DR, Schultz AJ, Siderius DW, Zuckerman DM

Living journal of computational molecular science.. 2018 1 (1)Epub 10/27/2018.

Minimal Nucleation State of ?-Synuclein Is Stabilized by Dynamic Threonine-Water Networks.

Romo TD, Lewis AK, Braun AR, Grossfield A, Sachs JN

ACS chemical neuroscience.. 2017 September 208 (9):1859-1864. Epub 07/10/2017.

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH

Journal of chemical theory and computation.. 2017 February 1413 (2):900-915. Epub 01/24/2017.

Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity.

Lin D, Grossfield A

Biophysical journal.. 2015 August 18109 (4):750-9. Epub 1900 01 01.

Retinal Conformation Changes Rhodopsin's Dynamic Ensemble.

Leioatts N, Romo TD, Danial SA, Grossfield A

Biophysical journal.. 2015 August 4109 (3):608-17. Epub 1900 01 01.

Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

Romo TD, Leioatts N, Grossfield A

Journal of computational chemistry.. 2014 December 1535 (32):2305-18. Epub 10/18/2014.

Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity.

Lin D, Grossfield A

Biophysical journal.. 2014 October 21107 (8):1862-1872. Epub 1900 01 01.

Structure-based simulations reveal concerted dynamics of GPCR activation.

Leioatts N, Suresh P, Romo TD, Grossfield A

Proteins.. 2014 October 82 (10):2538-51. Epub 06/09/2014.

Structural basis of G protein-coupled receptor-Gi protein interaction: formation of the cannabinoid CB2 receptor-Gi protein complex.

Mnpotra JS, Qiao Z, Cai J, Lynch DL, Grossfield A, Leioatts N, Hurst DP, Pitman MC, Song ZH, Reggio PH

The Journal of biological chemistry.. 2014 July 18289 (29):20259-72. Epub 05/22/2014.

How fast is your camera? Timescales for molecular motion and their role in restraining molecular dynamics.

Romo TD, Grossfield A

Biophysical journal.. 2014 June 17106 (12):2549-51. Epub 1900 01 01.

Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations.

Romo TD, Grossfield A

Biophysical journal.. 2014 April 15106 (8):1553-4. Epub 1900 01 01.

Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations.

Kimura T, Vukoti K, Lynch DL, Hurst DP, Grossfield A, Pitman MC, Reggio PH, Yeliseev AA, Gawrisch K

Proteins.. 2014 March 82 (3):452-65. Epub 10/17/2013.

Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures.

Leioatts N, Mertz B, Martinez-Mayorga K, Romo TD, Pitman MC, Feller SE, Grossfield A, Brown MF

Biochemistry.. 2014 January 2153 (2):376-85. Epub 01/08/2014.

Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin.

Horn JN, Kao TC, Grossfield A

Advances in experimental medicine and biology.. 2014 796 :75-94. Epub 1900 01 01.

Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics.

Horn JN, Cravens A, Grossfield A

Biophysical journal.. 2013 October 1105 (7):1612-23. Epub 1900 01 01.

The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures.

Seckler JM, Leioatts N, Miao H, Grossfield A

Proteins.. 2013 October 81 (10):1792-801. Epub 08/16/2013.

Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics.

Horn JN, Romo TD, Grossfield A

Biochemistry.. 2013 August 2052 (33):5604-10. Epub 08/09/2013.

Special issue on lipid-protein interactions.

Grossfield A

Chemistry and physics of lipids.. 2013 April 169 :1. Epub 1900 01 01.

Elastic Network Models are Robust to Variations in Formalism.

Leioatts N, Romo TD, Grossfield A

Journal of chemical theory and computation.. 2012 July 108 (7):2424-2434. Epub 06/05/2012.

Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes.

Olausson BE, Grossfield A, Pitman MC, Brown MF, Feller SE, Vogel A

Journal of the American Chemical Society.. 2012 March 7134 (9):4324-31. Epub 02/22/2012.

Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics.

Horn JN, Sengillo JD, Lin D, Romo TD, Grossfield A

Biochimica et biophysica acta.. 2012 February 1818 (2):212-8. Epub 07/28/2011.

Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation.

Romo TD, Grossfield A

Journal of chemical theory and computation.. 2011 August 97 (8):2464-72. Epub 07/01/2011.

Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.

Romo TD, Bradney LA, Greathouse DV, Grossfield A

Biochimica et biophysica acta.. 2011 August 1808 (8):2019-30. Epub 04/06/2011.

Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations.

Grossfield A

Biochimica et biophysica acta.. 2011 July 1808 (7):1868-78. Epub 04/03/2011.

Validating and improving elastic network models with molecular dynamics simulations.

Romo TD, Grossfield A

Proteins.. 2011 January 79 (1):23-34. Epub 09/24/2010.

A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor.

Hurst DP, Grossfield A, Lynch DL, Feller S, Romo TD, Gawrisch K, Pitman MC, Reggio PH

The Journal of biological chemistry.. 2010 June 4285 (23):17954-64. Epub 03/10/2010.

Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics.

Romo TD, Grossfield A, Pitman MC

Biophysical journal.. 2010 January 698 (1):76-84. Epub 1900 01 01.

Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations.

Khelashvili G, Grossfield A, Feller SE, Pitman MC, Weinstein H

Proteins.. 2009 August 176 (2):403-17. Epub 1900 01 01.

Quantifying uncertainty and sampling quality in biomolecular simulations.

Grossfield A, Zuckerman DM

Annual reports in computational chemistry. 2009 January 15 :23-48. Epub 1900 01 01.

LOOS: an extensible platform for the structural analysis of simulations.

Romo TD, Grossfield A

Annual International Conference of the IEEE Engineering in Medicine and Biology Society.. 2009 2009 :2332-5. Epub 1900 01 01.

Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin.

Grossfield A, Pitman MC, Feller SE, Soubias O, Gawrisch K

Journal of molecular biology.. 2008 August 29381 (2):478-86. Epub 05/22/2008.

Base flipping of the thymine dimer in duplex DNA.

O'Neil LL, Grossfield A, Wiest O

The journal of physical chemistry. B. 2007 October 11111 (40):11843-9. Epub 09/15/2007.

Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations.

Lau PW, Grossfield A, Feller SE, Pitman MC, Brown MF

Journal of molecular biology.. 2007 September 28372 (4):906-917. Epub 06/26/2007.

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M

Biophysical journal.. 2007 June 192 (11):3817-29. Epub 03/09/2007.

Convergence of molecular dynamics simulations of membrane proteins.

Grossfield A, Feller SE, Pitman MC

Proteins.. 2007 April 167 (1):31-40. Epub 1900 01 01.

Retinal counterion switch mechanism in vision evaluated by molecular simulations.

Martínez-Mayorga K, Pitman MC, Grossfield A, Feller SE, Brown MF

Journal of the American Chemical Society.. 2006 December 27128 (51):16502-3. Epub 1900 01 01.

Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential.

Jiao D, King C, Grossfield A, Darden TA, Ren P

The journal of physical chemistry. B. 2006 September 21110 (37):18553-9. Epub 1900 01 01.

Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation.

Grossfield A, Feller SE, Pitman MC

The journal of physical chemistry. B. 2006 May 11110 (18):8907-9. Epub 1900 01 01.

A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids.

Grossfield A, Feller SE, Pitman MC

Proceedings of the National Academy of Sciences of the United States of America.. 2006 March 28103 (13):4888-93. Epub 03/17/2006.

Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment.

Pitman MC, Grossfield A, Suits F, Feller SE

Journal of the American Chemical Society.. 2005 April 6127 (13):4576-7. Epub 1900 01 01.

Dependence of ion hydration on the sign of the ion's charge.

Grossfield A

The Journal of chemical physics.. 2005 January 8122 (2):024506. Epub 1900 01 01.

Role of solvent in determining conformational preferences of alanine dipeptide in water.

Drozdov AN, Grossfield A, Pappu RV

Journal of the American Chemical Society.. 2004 March 3126 (8):2574-81. Epub 1900 01 01.

Ion solvation thermodynamics from simulation with a polarizable force field.

Grossfield A, Ren P, Ponder JW

Journal of the American Chemical Society.. 2003 December 17125 (50):15671-82. Epub 1900 01 01.

Dipole lattice membrane model for protein calculations.

Grossfield A, Sachs J, Woolf TB

Proteins.. 2000 November 141 (2):211-23. Epub 1900 01 01.

Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations.

Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB

Journal of molecular biology.. 2000 September 22302 (3):727-46. Epub 1900 01 01.

Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations.

Woolf TB, Grossfield A, Tychko M

Biophysical journal.. 2000 February 78 (2):608-25. Epub 1900 01 01.