Publications 1997 2017

2017
2 Citations
proteins
Refinement
Proteins
Protein structure
sampling

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Feig, M., Yu, I., Wang, P. H., Nawrocki, G. & Sugita, Y. Aug 31 2017 In : Journal of Physical Chemistry B. 121, 34, p. 8009-8025 17 p.

Research output: Contribution to journalArticle

crowding
Spontaneous Fractures
Computer Simulation
Peptides
Proteins

Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions

Dutagaci, B., Wittayanarakul, K., Mori, T. & Feig, M. Jun 13 2017 In : Journal of Chemical Theory and Computation. 13, 6, p. 3049-3059 11 p.

Research output: Contribution to journalArticle

membranes
Anthralin
Bronchiolo-Alveolar Adenocarcinoma
Membranes
scoring
2 Citations
Membrane
Bronchiolo-Alveolar Adenocarcinoma
Membranes
Model
Anthralin
1 Citations

Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding

Wang, P. H., Yu, I., Feig, M. & Sugita, Y. Mar 1 2017 In : Chemical Physics Letters. 671, p. 63-70 8 p.

Research output: Contribution to journalArticle

proteins
crowding
hydration
Hydration
water

Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity

Wang, B., Sexton, R. E. & Feig, M. Apr 1 2017 In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1860, 4, p. 482-490 9 p.

Research output: Contribution to journalArticle

DNA-Directed RNA Polymerases
Catalytic Domain
Nucleotides
Kinetics
Learned Helplessness
2016
12 Citations

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

Yu, I., Mori, T., Ando, T., Harada, R., Jung, J., Sugita, Y. & Feig, M. Nov 1 2016 In : eLife. 5, NOVEMBER2016, e19274

Research output: Contribution to journalArticle

Cytoplasm
Proteins
MSH Release-Inhibiting Hormone
Anthralin
Ligands
25 Citations

CHARMM36m: An improved force field for folded and intrinsically disordered proteins

Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., De Groot, B. L., Grubmüller, H. & MacKerell, A. D. Dec 29 2016 In : Nature Methods. 14, 1, p. 71-73 3 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Peptides
Proteins
Killer Whale
Atoms
5 Citations

DnaC traps DnaB as an open ring and remodels the domain that binds primase

Chodavarapu, S., Jones, A. D., Feig, M. & Kaguni, J. M. Jan 8 2016 In : Nucleic Acids Research. 44, 1, p. 210-220 11 p.

Research output: Contribution to journalArticle

DNA Primase
DNA Helicases
Replication Origin
Deuterium
DNA Replication
2 Citations

Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation

Ochieng, P. O., White, N. A., Feig, M. & Hoogstraten, C. G. Oct 27 2016 In : Journal of Physical Chemistry B. 120, 42, p. 10885-10898 14 p.

Research output: Contribution to journalArticle

Catalytic RNA
Base Pairing
RNA
Sampling
Eosinophil Chemotactic Factors
3 Citations

Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD

Feig, M. Jul 25 2016 In : Journal of Chemical Information and Modeling. 56, 7, p. 1304-1312 9 p.

Research output: Contribution to journalArticle

structure
method
Anthralin
Proteins
model
1 Citations

Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways

Wang, B., Francis, J., Sharma, M., Law, S. M., Predeus, A. V. & Feig, M. Oct 1 2016 In : PLoS Computational Biology. 12, 10, e1005159

Research output: Contribution to journalArticle

Pathway
Range of data
Melanocyte-Stimulating Hormones
Adenosine Triphosphatases
adenosinetriphosphatase
13 Citations

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Mori, T., Miyashita, N., Im, W., Feig, M. & Sugita, Y. Jul 1 2016 In : Biochimica et Biophysica Acta - Biomembranes. 1858, 7, p. 1635-1651 17 p.

Research output: Contribution to journalReview article

Molecular Dynamics Simulation
Membrane Proteins
Membranes
Anthralin
Beta-Globulins
2015
16 Citations

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

Feig, M., Harada, R., Mori, T., Yu, I., Takahashi, K. & Sugita, Y. 2015 In : Journal of Molecular Graphics and Modelling. 58, p. 1-9 9 p.

Research output: Contribution to journalArticle

Anthralin
cytoplasm
genes
Cyclic AMP Receptor Protein
Genes
8 Citations

Density-biased sampling: A robust computational method for studying pore formation in membranes

Mirjalili, V. & Feig, M. Jan 13 2015 In : Journal of Chemical Theory and Computation. 11, 1, p. 343-350 8 p.

Research output: Contribution to journalArticle

sampling
membranes
porosity
Beta-Globulins
Bronchiolo-Alveolar Adenocarcinoma
5 Citations

Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details

Wang, B., Opron, K., Burton, Z. F., Cukier, R. I. & Feig, M. Jan 30 2015 In : Nucleic Acids Research. 43, 2, p. 1133-1146 14 p.

Research output: Contribution to journalArticle

DNA-Directed RNA Polymerases
Catalytic Domain
Molecular Dynamics Simulation
Catalysis
Nucleotides
19 Citations

GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Jung, J., Mori, T., Kobayashi, C., Matsunaga, Y., Yoda, T., Feig, M. & Sugita, Y. Jul 1 2015 In : Wiley Interdisciplinary Reviews: Computational Molecular Science. 5, 4, p. 310-323 14 p.

Research output: Contribution to journalArticle

Model
Airway Obstruction
simulation
Molecular Dynamics Simulation
Anthralin
5 Citations

Interactions of amino acid side-chain analogs within membrane environments

Mirjalili, V. & Feig, M. Feb 19 2015 In : Journal of Physical Chemistry B. 119, 7, p. 2877-2885 9 p.

Research output: Contribution to journalArticle

membranes
Bronchiolo-Alveolar Adenocarcinoma
Membranes
interactions
amino acids
7 Citations

Molecular evidence for functional divergence and decay of a transcription factor derived from whole- genome duplication in Arabidopsis thaliana

Lehti-Shiu, M. D., Uygun, S., Moghe, G. D., Panchy, N., Fang, L., Hufnagel, D. E., Jasicki, H. L., Feig, M. & Shiu, S. H. Aug 1 2015 In : Plant Physiology. 168, 4, p. 1717-1734 18 p.

Research output: Contribution to journalArticle

Arabidopsis
Transcription Factors
Genome
transcription factors
Arabidopsis thaliana
10 Citations

Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease

Farrugia, M. A., Wang, B., Feig, M. & Hausinger, R. P. Oct 20 2015 In : Biochemistry. 54, 41, p. 6392-6401 10 p.

Research output: Contribution to journalArticle

Enterobacter aerogenes
Urease
Nickel
Communication Disorders
Apoproteins
7 Citations
Nerve Crush
Cholesterol
Molecular Dynamics Simulation
Proteins
Beta-Globulins
1 Citations

Role of the n + 1 amino acid residue on the deamidation of asparagine in pentapeptides

Ince, H. H., Konuklar, F. A. S., Ugur, I., Ozcan, . A., Sayadi, M., Feig, M. & Aviyente, V. Dec 2 2015 In : Molecular Physics. 113, 23, p. 3839-3848 10 p.

Research output: Contribution to journalArticle

peptides
water
Asparagine
Amino Acids
Peptides
3 Citations

The evolutionary conserved C-terminal domains in the mammalian retinoblastoma tumor suppressor family serve as dual regulators of protein stability and transcriptional potency

Sengupta, S., Lingnurkar, R., Carey, T. S., Pomaville, M., Kar, P., Feig, M., Wilson, C. A., Knott, J. G., Arnosti, D. N. & Henry, R. W. Jun 5 2015 In : Journal of Biological Chemistry. 290, 23, p. 14462-14475 14 p.

Research output: Contribution to journalArticle

Retinoblastoma
Protein Stability
Neoplasms
Bibliography of Medicine
Proteasome Endopeptidase Complex
2014
1 Citations
Palmitates
Phosphotransferases
Fatty Acids
Binding Sites
Ligands
7 Citations

Conformational preferences of DNA in reduced dielectric environments

Yildirim, A., Sharma, M., Varner, B. M., Fang, L. & Feig, M. Aug 28 2014 In : Journal of Physical Chemistry B. 118, 37, p. 10874-10881 8 p.

Research output: Contribution to journalArticle

DNA
deoxyribonucleic acid
simulation
Sampling
Beta-Globulins
5 Citations

Differential mismatch recognition specificities of eukaryotic MutS homologs, MutSα and MutSβ

Sharma, M., Predeus, A. V., Kovacs, N. & Feig, M. Jun 3 2014 In : Biophysical Journal. 106, 11, p. 2483-2492 10 p.

Research output: Contribution to journalArticle

DNA
Nucleotides
Molecular Dynamics Simulation
Substrate Specificity
Eukaryota
34 Citations

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

Mirjalili, V., Noyes, K. & Feig, M. Feb 2014 In : Proteins: Structure, Function and Bioinformatics. 82, SUPPL.2, p. 196-207 12 p.

Research output: Contribution to journalArticle

Physics
Molecular Dynamics Simulation
Molecular Structure
Proteins
Nerve Crush
9 Citations

Recent advances in transferable coarse-grained modeling of proteins

Kar, P. & Feig, M. 2014 In : Advances in Protein Chemistry and Structural Biology. 96, p. 143-180 38 p.

Research output: Contribution to journalArticle

Proteins
Anthralin
Biochemical Processes
Computer Simulation
Dibenzoxepins
12 Citations

Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation

Taylor, K. A., Feig, M., Brooks, C. L., Fagnant, P. M., Lowey, S. & Trybus, K. M. Mar 2014 In : Journal of Structural Biology. 185, 3, p. 375-382 8 p.

Research output: Contribution to journalArticle

Myosin Light Chains
Phosphorylation
Myosin Heavy Chains
Serine
Myosin Type II
10 Citations

Transferring the PRIMO coarse-grained force field to the membrane environment: Simulations of membrane proteins and helix-helix association

Kar, P., Gopal, S. M., Cheng, Y. M., Panahi, A. & Feig, M. Aug 12 2014 In : Journal of Chemical Theory and Computation. 10, 8, p. 3459-3472 14 p.

Research output: Contribution to journalArticle

membranes
Bronchiolo-Alveolar Adenocarcinoma
Membranes
peptides
proteins
2013
9 Citations

Computational simulation strategies for analysis of multisubunit RNA polymerases

Wang, B., Feig, M., Cukier, R. I. & Burton, Z. F. Nov 13 2013 In : Chemical Reviews. 113, 11, p. 8546-8566 21 p.

Research output: Contribution to journalArticle

Common Bile Duct Diseases
Aminopyrine
Spontaneous Fractures
Autistic Disorder
Computational methods
16 Citations

DNA bending propensity in the presence of base mismatches: Implications for DNA repair

Sharma, M., Predeus, A. V., Mukherjee, S. & Feig, M. May 23 2013 In : Journal of Physical Chemistry B. 117, 20, p. 6194-6205 12 p.

Research output: Contribution to journalArticle

DNA
deoxyribonucleic acid
Repair
purines
pyrimidines
25 Citations
Bronchiolo-Alveolar Adenocarcinoma
membranes
Membranes
Anthralin
Hemerythrin
14 Citations

Energetic and structural details of the trigger-loop closing transition in RNA polymerase II

Wang, B., Predeus, A. V., Burton, Z. F. & Feig, M. Aug 6 2013 In : Biophysical Journal. 105, 3, p. 767-775 9 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Nucleosides
Molecular Dynamics Simulation
Catalysis
Eukaryota
27 Citations

Interionic hydration structures of NaCl in aqueous solution: A combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations

Ghosh, M. K., Re, S., Feig, M., Sugita, Y. & Choi, C. H. Jan 10 2013 In : Journal of Physical Chemistry B. 117, 1, p. 289-295 7 p.

Research output: Contribution to journalArticle

Hydration
hydration
ions
Ions
Hexosaminidase A
35 Citations

PRIMO: A transferable coarse-grained force field for proteins

Kar, P., Gopal, S. M., Cheng, Y. M., Predeus, A. & Feig, M. Aug 13 2013 In : Journal of Chemical Theory and Computation. 9, 8, p. 3769-3788 20 p.

Research output: Contribution to journalArticle

proteins
Proteins
field theory (physics)
Anthralin
molecular dynamics
31 Citations

Protein structure refinement through structure selection and averaging from molecular dynamics ensembles

Mirjalili, V. & Feig, M. Feb 12 2013 In : Journal of Chemical Theory and Computation. 9, 2, p. 1294-1303 10 p.

Research output: Contribution to journalArticle

molecular dynamics
Nerve Crush
Molecular dynamics
set theory
interpolation
24 Citations

Reaching new levels of realism in modeling biological macromolecules in cellular environments

Feig, M. & Sugita, Y. 2013 In : Journal of Molecular Graphics and Modelling. 45, p. 144-156 13 p.

Research output: Contribution to journalArticle

Anthralin
Biomolecules
Dibenzoxepins
Erysipeloid
Bibliography of Medicine
68 Citations

Reduced native state stability in crowded cellular environment due to protein-protein interactions

Harada, R., Tochio, N., Kigawa, T., Sugita, Y. & Feig, M. Mar 6 2013 In : Journal of the American Chemical Society. 135, 9, p. 3696-3701 6 p.

Research output: Contribution to journalArticle

Proteins
Nuclear magnetic resonance
Bibliography of Medicine
Dapsone
Protein Stability
11 Citations
Phosphorylation
Paranasal Sinus Neoplasms
Sarcoplasmic Reticulum Calcium-Transporting ATPases
Computer Simulation
Membranes
15 Citations

Solvent electronic polarization effects on Na+-Na+ and Cl--Cl- pair associations in aqueous solution

Choi, C. H., Re, S., Rashid, M. H. O., Li, H., Feig, M. & Sugita, Y. Aug 8 2013 In : Journal of Physical Chemistry B. 117, 31, p. 9273-9279 7 p.

Research output: Contribution to journalArticle

molecular dynamics
Nerve Crush
Molecular dynamics
aqueous solutions
polarization
2012
29 Citations

Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations

Predeus, A. V., Gul, S., Gopal, S. M. & Feig, M. Jul 26 2012 In : Journal of Physical Chemistry B. 116, 29, p. 8610-8620 11 p.

Research output: Contribution to journalArticle

crowding
peptides
proteins
simulation
Peptides
48 Citations

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

Best, R. B., Mittal, J., Feig, M. & MacKerell, A. D. Sep 5 2012 In : Biophysical Journal. 103, 5, p. 1045-1051 7 p.

Research output: Contribution to journalArticle

Inclusion Bodies
Proteins
Dipeptides
Intrinsically Disordered Proteins
Protein Folding
3 Citations

Molecular dynamics trajectory compression with a coarse-grained model

Cheng, Y. M., Gopal, S. M., Law, S. M. & Feig, M. 2012 In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9, 2, p. 476-486 11 p., 6051427

Research output: Contribution to journalArticle

Trajectory
Data Compression
Molecular Dynamics Simulation
Trajectories
Compression
661 Citations

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ 1 and χ 2 Dihedral Angles

Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M. & MacKerell, A. D. Sep 11 2012 In : Journal of Chemical Theory and Computation. 8, 9, p. 3257-3273 17 p.

Research output: Contribution to journalArticle

proteins
Proteins
simulation
Nuclear magnetic resonance
Anthralin
62 Citations

Protein crowding affects hydration structure and dynamics

Harada, R., Sugita, Y. & Feig, M. Mar 14 2012 In : Journal of the American Chemical Society. 134, 10, p. 4842-4849 8 p.

Research output: Contribution to journalArticle

Spontaneous Fractures
Proteins
Crowding
Water
Hydration
21 Citations

Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water

Choi, C. H., Re, S., Feig, M. & Sugita, Y. Jun 29 2012 In : Chemical Physics Letters. 539-540, p. 218-221 4 p.

Research output: Contribution to journalArticle

molecular dynamics
Nerve Crush
fragments
protons
water
59 Citations

Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding

Feig, M. & Sugita, Y. Jan 12 2012 In : Journal of Physical Chemistry B. 116, 1, p. 599-605 7 p.

Research output: Contribution to journalArticle

crowding
lysozyme
inhibitors
Enzymes
albumins
2011
12 Citations

Base-flipping mechanism in postmismatch recognition by Muts

Law, S. M. & Feig, M. 2011 In : Biophysical Journal. 101, 9, p. 2223-2231 9 p.

Research output: Contribution to journalArticle

DNA
Molecular Dynamics Simulation
Hydrogen Bonding
Eukaryota
Genome
4 Citations

Conformational sampling in structure prediction and refinement with atomistic and coarse-grained models

Feig, M., Gopal, S. M., Vadivel, K. & Stumpff-Kane, A. 2011 Multiscale Approaches to Protein Modeling: Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies. Springer New York, p. 85-109 25 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Anthralin
Proteins
Atoms
Beta-Globulins
Birth Injuries