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1

Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

Zerze, Gül H., Miller, Cayla M., Granata, Daniele, Mittal, Jeetain

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 966 KB

english, 2015

2

Highly Disordered Amyloid- β Monomer Probed by Single-Molecule FRET and MD Simulation

Meng, Fanjie, Bellaiche, Mathias M.J., Kim, Jae-Yeol, Zerze, Gül H., Best, Robert B., Chung, Hoi Sung

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 3.49 MB

english, 2018

3

Correlation of Helical Propensity in Amylin Sequences with Known Aggregation Propensity

Zerze, Gül H., Miller, Cayla, Mittal, Jeetain

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 38 KB

english, 2014

4

Molecular Simulations Indicate Marked Differences in the Structure of Amylin Mutants, Correlated with Known Aggregation Propensity

Miller, Cayla, Zerze, Gül H., Mittal, Jeetain

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 4.94 MB

english, 2013

5

Modest Influence of FRET Chromophores on the Properties of Unfolded Proteins

Zerze, Gül H., Best, Robert B., Mittal, Jeetain

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

6

Correction to “Molecular Simulations Indicate Marked Differences in the Structure of Amylin Mutants, Correlated with Known Aggregation Propensity”

Miller, Cayla, Zerze, Gül H., Mittal, Jeetain

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 1.11 MB

english, 2014

7

Effect of co-substrate sorbitol different feeding strategies on human growth hormone production by recombinant Pichia pastoris

Çalık, Pınar, Bozkurt, Bahar, Zerze, Gül H., İnankur, Bahar, Bayraktar, Eda, Boy, Erdem, Orman, Mehmet Ali, Açık, Eda, Özdamar, Tunçer H.

Journal:

Journal of Chemical Technology & Biotechnology

Year:

2013

Language:

english

File:

PDF, 425 KB

english, 2013

8

Recombinant protein production in Pichia pastoris under glyceraldehyde-3-phosphate dehydrogenase promoter: From carbon source metabolism to bioreactor operation parameters

Çalık, Pınar, Ata, Özge, Güneş, Hande, Massahi, Aslan, Boy, Erdem, Keskin, Abdullah, Öztürk, Sibel, Zerze, Gül H., Özdamar, Tunçer H.

Journal:

Biochemical Engineering Journal

Year:

2015

Language:

english

File:

PDF, 2.66 MB

english, 2015

9

Methanol feeding strategy design enhances recombinant human growth hormone production by Pichia pastoris

Güneş, Hande, Boy, Erdem, Ata, Özge, Zerze, Gül H, Çalık, Pınar, Özdamar, Tunçer H

Journal:

Journal of Chemical Technology & Biotechnology

Year:

2015

Language:

english

File:

PDF, 1.45 MB

english, 2015

10

To what extent does surface hydrophobicity dictate peptide folding and stability near surfaces?

Zerze, Gül H., Mullen, Ryan G., Levine, Zachary A., Shea, Joan-Emma, Mittal, Jeetain

Journal:

Year:

2015

Language:

english

File:

PDF, 2.66 MB

english, 2015

11

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations

Zerze, Gül H., Best, Robert B, Mittal, Jeetain

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 2.88 MB

english, 2015

12

Effect of O-linked Glycosylation on the Equilibrium Structural Ensemble of Intrinsically Disordered Polypeptides

Zerze, Gül H., Mittal, Jeetain

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 2.25 MB

english, 2015

13

Comparing Solution Structures of Amylin and CGRP by Nanosecond Laser-Pump Spectroscopy and Atomistic Simulations

Sizemore, Sara M., Zerze, Gül H., Cope, Stephanie M., Mittal, Jeetain, Vaiana, Sara M.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 57 KB

english, 2015

14

Diffusive Dynamics of Contact Formation in Disordered Polypeptides

Zerze, Gül H., Mittal, Jeetain, Best, Robert B.

Journal:

Physical Review Letters

Year:

2016

Language:

english

File:

PDF, 536 KB

english, 2016

15

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces

Levine, Zachary A., Rapp, Michael V., Wei, Wei, Mullen, Ryan Gotchy, Wu, Chun, Zerze, Gül H., Mittal, Jeetain, Waite, J. Herbert, Israelachvili, Jacob N., Shea, Joan-Emma

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.38 MB

english, 2016

16

Dynamics of Contact Formation in Disordered Polypeptides

Zerze, Gül H., Best, Robert B., Mittal, Jeetain

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 38 KB

english, 2016

17

Molecular Simulations of Unfolded and Intrinsically Disordered Proteins

Zerze, Gül H., Best, Robert B., Mittal, Jeetain

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 33 KB

english, 2015

18

Folding thermodynamics of β -hairpins studied by replica-exchange molecular dynamics simulations

Zerze, Gül H., Uz, Bilge, Mittal, Jeetain

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 629 KB

english, 2015

19

ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain

Conicella, Alexander E., Zerze, Gül H., Mittal, Jeetain, Fawzi, Nicolas L.

Journal:

Year:

2016

Language:

english

File:

PDF, 4.37 MB

english, 2016

20

A carbon nanotube reporter of microRNA hybridization events in vivo

Harvey, Jackson D., Jena, Prakrit V., Baker, Hanan A., Zerze, Gül H., Williams, Ryan M., Galassi, Thomas V., Roxbury, Daniel, Mittal, Jeetain, Heller, Daniel A.

Journal:

Nature Biomedical Engineering

Year:

2017

Language:

english

File:

PDF, 3.00 MB

english, 2017

21

Intrinsically Disordered Protein Dynamics Uncovered through Dynamic Flexibility Index (DFI) Analysis

Modi, Tushar, Zerze, Gül H., Mittal, Jeetain, Vaiana, Sara M., Ozkan, S. Banu

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 62 KB

english, 2017

22

Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity

Monahan, Zachary, Ryan, Veronica H, Janke, Abigail M, Burke, Kathleen A, Rhoads, Shannon N, Zerze, Gül H, O'Meally, Robert, Dignon, Gregory L, Conicella, Alexander E, Zheng, Wenwei, Best, Robert B, Co

Journal:

The EMBO Journal

Year:

2017

Language:

english

File:

PDF, 2.29 MB

english, 2017

23

Interplay Between Membrane Composition and Structural Stability of Membrane-Bound IAPP

Dignon, Gregory L, Zerze, Gül H., Mittal, Jeetain

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 1.68 MB

english, 2017

24

Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation

Ryan, Veronica H., Dignon, Gregory L., Zerze, Gül H., Chabata, Charlene V., Silva, Rute, Conicella, Alexander E., Amaya, Joshua, Burke, Kathleen A., Mittal, Jeetain, Fawzi, Nicolas L.

Journal:

Year:

2018

Language:

english

File:

PDF, 4.30 MB

english, 2018

25

Inferring Properties of Disordered Chains From FRET Transfer Efficiencies

Zheng, Wenwei, Zerze, Gül, Borgia, Alessandro, Mittal, Jeetain, Schuler, Benjamin, Best, Robert B.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 43 KB

english, 2018

26

Inferring properties of disordered chains from FRET transfer efficiencies

Zheng, Wenwei, Zerze, Gül H., Borgia, Alessandro, Mittal, Jeetain, Schuler, Benjamin, Best, Robert B.

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 1.59 MB

english, 2018

27

Computational modeling highlights the role of the disordered Formin Homology 1 domain in profilin-actin transfer

Horan, Brandon G., Zerze, Gül H., Kim, Young C., Vavylonis, Dimitrios, Mittal, Jeetain

Journal:

Year:

2018

Language:

english

File:

PDF, 2.66 MB

english, 2018

28

Electrostatic Screening Modulates Analyte Binding and Emission of Carbon Nanotubes

Harvey, Jackson D., Zerze, Gül H., Tully, Kathryn M., Mittal, Jeetain, Heller, Daniel A.

Journal:

The Journal of Physical Chemistry C

Year:

2018

Language:

english

File:

PDF, 2.23 MB

english, 2018

29

Computational Investigation of the Effect of Backbone Chiral Inversions on Polypeptide Structure

Zerze, Gül H., Khan, Mohammad Navaid, Stillinger, Frank H., Debenedetti, Pablo G.

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 3.35 MB

english, 2018

30

Multiscale Model of the Formin Homology 1 Domain Illustrates its Role in Regulation of Actin Polymerization

Horan, Brandon G., Zerze, Gül, Dignon, Gregory L., Kim, Young C., Vavylonis, Dimitrios, Mittal, Jeetain

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 47 KB

english, 2018

31

Effect of heterochiral inversions on the structure of a β -hairpin peptide

Zerze, Gül H., Stillinger, Frank H., Debenedetti, Pablo G.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2019

Language:

english

File:

PDF, 5.55 MB

english, 2019

32

Evolution of All-atom Protein Force Fields to Improve Local and Global Properties

Zerze, Gül H., Zheng, Wenwei, Best, Robert B., Mittal, Jeetain

Journal:

The Journal of Physical Chemistry Letters

Year:

2019

Language:

english

File:

PDF, 1.77 MB

english, 2019

33

Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain

Murthy, Anastasia C., Dignon, Gregory L., Kan, Yelena, Zerze, Gül H., Parekh, Sapun H., Mittal, Jeetain, Fawzi, Nicolas L.

Journal:

Nature Structural and Molecular Biology

Year:

2019

Language:

english

File:

PDF, 5.81 MB

english, 2019

34

Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain

Murthy, Anastasia C., Dignon, Gregory L., Kan, Yelena, Zerze, Gül H., Parekh, Sapun H., Mittal, Jeetain, Fawzi, Nicolas L.

Journal:

Nature Structural and Molecular Biology

Year:

2019

File:

PDF, 5.81 MB

2019

35

Computational investigation of retro‐isomer equilibrium structures: Intrinsically disordered, foldable and cyclic peptides

Zerze, Gül H., Stillinger, Frank H., Debenedetti, Pablo G.

Journal:

Year:

2019

Language:

english

File:

PDF, 1.96 MB

english, 2019