Phanourios Tamamis Lab

Artie McFerrin Department of Chemical Engineering

Texas A&M University

We use simulations to uncover or modulate biological Interactions, design novel peptide- and clay-materials, and investigate biological self-assembly.

Home

Bio

News-Announcements

Lab Members

Research

Patents-Publications

Funding

Home

Our Approach and Our Goals

Computational methods, including molecular dynamics (MD) simulations and free energy calculations, are increasingly becoming powerful tools in the fields of protein structure prediction and de novo protein design. Despite the continuous advancement of experimental methods, computational tools have proved to be of utmost importance to fill crucial “gaps”, obtain information that is not accessible from experiments, solve critical problems in biology, and lead to the discovery of novel materials and therapeutics. We use simulations and develop novel simulation-based tools, combining biophysical-chemistry and engineering, optimization-based, principles, our lab aims to:

 

• Study self-assembly and design novel functional peptide-materials with applications as tissue engineering agents, drug-nanocarriers and environmental sorbents.

• Study amyloid inhibition, and design novel amyloid inhibitors for diabetes type 2, Alzheimer’s and Parkinson’s diseases.

• Study interactions between proteins and chemical compounds, modified RNAs and modified DNAs, associated with important functions in biology and health.

• Study interactions between toxic compounds and sorbent materials including clays, and design novel multicomponent sorbents. 

 

Phanourios Tamamis

 

image001

Assistant Professor

 

Artie McFerrin Department of Chemical Engineering

 

Texas A&M University

 

Lab Office: 330 GERB,

Teaching Office: 225 JEB

 

3122 TAMU, College Station,

TX 77843

 

tamamis@tamu.edu

Phone: 979-862-1610

Fax: 979-845-6446

 

Phanourios Tamamis - Short Bio

Phanourios Tamamis received his B.S. degree in 2006 (excellent; top academic performance) and Ph.D. degree in 2010 from the Physics Department of the University of Cyprus, and was recognized as the top Cypriot undergraduate researcher in 2006. During his undergraduate, graduate and early-postdoctoral studies, he was supervised by Professor Georgios Archontis. After finishing his Ph.D. studies, from 2010 until 2012, Phanourios Tamamis served as a Postdoctoral Fellow at the University of Cyprus, and as a Fulbright scholar at the University of California at Riverside and Princeton University, under the co-supervision of Professors Dimitrios Morikis and Christodoulos A. Floudas. He was recognized as an “Outstanding Young Researcher” in the 2012 Computational Biophysics to Systems Biology conference. In 2013, he joined the lab of Professor Christodoulos A. Floudas at the Chemical and Biological Engineering Department of Princeton University as a Postdoctoral Research Associate. In 2015, he joined the Chemical Engineering Department of Texas A&M University as an Assistant Professor. Tamamis’ lab addresses key problems at the intersection of computational biophysics, computational biomolecular engineering and self-assembly. Among other, Tamamis’ lab has been developing pioneering tools enabling the study of modified RNAs and DNAs with proteins, facilitating the use of computers to functionalize-peptide materials as tissue engineering and drug nanocarriers, and enlightening how clays can be used and be improved to be be applied sorbents mitigating toxic compounds’ exposure. He received awards for both his research and teaching. Tamamis’ lab research is currently supported by the NSF and the NIH.

 

 

News and Announcements

Key stories from 2020

• Tamamis lab has welcomed two new PhD students, Busra Ozguney and Aswin Hanagal, and one new undergraduate student, Hannah Strong.

• Tamamis lab published nine papers in 2020. Our computational research was performed in collaboration with several experimental labs, including Drs. Phillips’, Safe’s and Jayaraman’s lab at Texas A&M University, Dr. Contreras’ lab at UT Austin, Dr. Gazit’s lab at Tel Aviv University, Dr. Mitraki’s lab at the University of Crete, and Dr. Gkikas’ lab at U. Mass. Lowell.

• Tamamis lab received funding from the NSF, on the study of RNA modifications with key protein readers and erasers.

 

 

Lab Members

PhD students

Asuka Orr

Asuka Orr (5th year PhD student)

Busra Ozguney (1st year PhD student)

Aswin Hanagal (1st year PhD student)

 

 

Undergraduate students

 

Joshua Griffith (4th year Undergrad.)

Hannah Strong (3rd year Undergrad.)

 

 

 

 

Research

Our Current Research Directions

Engineering peptide fibril-forming materials with applications in biomedicine, energy and environment

Computational methods possess the capacity to provide atomic-level insights into the structural organization of peptide self-assembled peptides and nanostructures. Our research aims at exploiting the self-assembly properties of peptides/proteins to engineer novel peptide materials with promising applications as tissue engineering agents, drug nanocarriers and sorbents for environmental applications.

 

Designing inhibitors of amyloid formation as potential therapeutics of amyloid diseases

Amyloid deposition in human tissue is associated with a number of diseases including all common dementias and diabetes. A critical initial step to prevent amyloid fibril formation is to delineate the self-assembly properties and provide insights into the structure of amyloid fibrils of the associated peptide or protein in each disease. Our research aims at (i) elucidating the amyloid structures formed by peptides and proteins, and (ii) designing protein and compound inhibitors of amyloid formation, which can be used as seeds for novel potential therapeutics for amyloid diseases, including Alzheimer’s, Parkinson’s and diabetes diseases. 

 

Uncovering biological interactions formed between proteins with compounds, modified RNAs or DNAs light into key biological axes.

Understanding how proteins bind to compounds modified RNAs and modified DNAs is of significant importance, as such interactions play a key role in living organisms’ biological processes. Our research aims to develop novel computational protocols investigating such interactions. We emphasize on investigating the formation of such interactions in systems of critical importance to biology and health. In addition, we utilize these interactions to study and design novel compounds inhibiting these interactions. These tools can be used as potential therapeutic compounds, or as “molecular tools” enabling researchers to monitor and study these interactions.

 

 Investigating the interactions of toxic compounds with clays, and designing novel advanced clay-based materials

Clays have the capacity to bind toxic compounds and have been used as sorbents mitigating toxic compounds. Our research aims to study such systems using molecular simulations, elucidate the key mechanisms of toxic compounds binding to clays or amended clays, and discover novel highly effective compounds as amendments enabling the binding of toxic compounds to clays.

 

Patents

 

Compstatin analogs, US Patent 9, 512, 180, 2016.

 

Amyloid peptide scaffolds coordinate with alzheimer's disease drugs. US Patent 62, 757, 384, 2018.

 

Publications

Peer-Reviewed Papers and Book Chapters

Publications of Tamamis lab

1. Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J., 2020, 118, 492-504.

 

2. Orr AA, He S, Wang M, Goodall A, Hearon SE, Phillips TD, Tamamis P. Insights into the interactions of bisphenol and phthalate compounds with unamended and carnitine-amended montmorillonite clays. Computers and Chemical Engineering, 2020, 143, 107063.

 

3. Chen Y, Orr AA, Tao K, Wang Z, Ruggiero A, Shimon LJW, Schnaider L, Goodall A, Rencus-Lazar S, Gilead S, Slutsky I, Tamamis P, Tan Z, Gazit E. High-Efficiency Fluorescence through Bioinspired Supramolecular Self-Assembly. ACS Nano. 2020, 14, 3, 2798-2807.

 

4. Tao K, Orr AA, Tian Z, Makam P, Gilead S, Si M, Rencus-Lazar S, Qu S, Zhang M, Tamamis P, Gazit P. Enhanced Fluorescence for Bioassembly by Environment-Switching Doping of Metal Ions. Adv. Funct. Mater. 2020, 1909614.

 

5. Gonzalez-Rivera JC, Orr AA, Engels SM, Jakubowski JM, Sherman MW, O'Connor KN, Matteson T, Woodcock BC, Contreras LM, Tamamis P. Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding. Computational and Structural Biotechnology Journal, 2020, 18, 137-152.

 

6. Jonnalagadda SVR, Gerace AJ, Thai K, Johnson J, Tsimenidis K, Jakubowski JM, Shen C, Henderson KJ, Tamamis P, Gkikas M. Amyloid Peptide Scaffolds Coordinate with Alzheimer's Disease Drugs. J Phys Chem B. 2020, 124, 487-503.

 

7. Wang M, Orr AA, Jakubowski JM, Bird KE, Casey CM, Hearon SE, Tamamis P, Phillips TD. Enhanced adsorption of per- and polyfluoroalkyl substances (PFAS) by edible, nutrient-amended montmorillonite clays. Water Research, 2020, 188, 116534. 

 

8. Park H, Jin UH, Karki K, Allred C, Davidson LA, Chapkin RS, Orr AA, Nowshad F, Jayaraman A, Tamamis P, Safe S. Hydroxylated Chalcones as Aryl Hydrocarbon Receptor Agonists: Structure-Activity Effects. Toxicological Sciences, 2020, kfaa179.

 

9. Kokotidou C, Tamamis P, Mitraki A. Amyloid-Like Peptide Aggregates. Peptide-based Biomaterials. 2020, 217-268.

 

10. Jakubowski JM, Orr AA, Le DA, Tamamis P. Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from MD Simulations. J Chem Inf Model. 2019, 60, 1, 289-305. 

 

11. Kokotidou C, Jonnalagadda SVR, Orr AA, Vrentzos G, Kretsovali A, Tamamis P, Mitraki A. Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles. Biomolecules. 2019 10(1). pii: E7.

 

12. Wang M, Orr AA, He S, Dalaijamts C, Weihsueh AC, Tamamis P, Phillips TD. Montmorillonites Can Tightly Bind Glyphosate and Paraquat Reducing Toxin Exposures and Toxicity. ACS Omega 2019, 4, 18, 17702-17713.

 

13. Park H, Jin UH, Orr AA, Echegaray SP, Davidson LA, Allred CD, Chapkin RS, Jayaraman A, Lee K, Tamamis P, Safe S. Isoflavones as Ah Receptor Agonists in Colon-Derived Cell Lines: Structure-Activity Relationships. Chem Res Toxicol. 2019, 32, 2353-2364.

 

14. Kokotidou C, Tamamis P, Mitraki A. SelfAssembling Amyloid Sequences as Scaffolds for Material Design: A Case Study of Building Blocks Inspired From the Adenovirus Fiber Protein. Macromolecular Symposia, 2019, 386, 1900005.

 

15.  Yoon K, Chen CC, Orr AA, Barreto PN, Tamamis P, Safe S. Activation of COUP-TFI by a Novel Diindolylmethane Derivative. Cells, 2019, 8, 220.

 

16. Jonnalagadda SVR, Kokotidou C, Orr AA, Fotopoulou E, Henderson KJ, Choi CH, Lim WT, Choi SJ, Jeong HK, Mitraki A, Tamamis P. Computational Design of Functional Amyloid Materials with Cesium Binding, Deposition and Capture Properties. J Phys Chem B. 2018, 122, 7555-7568.

 

17. Keasar C. et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports 2018, 8, 9939.

 

18. Mohan RR, Wilson M, Gorham RD Jr, Harrison RES, Morikis VA, Kieslich CA, Orr AA, Coley AV, Tamamis P, Morikis D. Virtual Screening of Chemical Compounds for Discovery of Complement C3 Ligands. ACS Omega, 2018, 3, 6427–6438.

 

19. Kokotidou C, Jonnalagadda SVR, Orr AA, Seoane-Blanco M, Apostolidou CP, van Raaij MJ, Kotzabasaki M, Chatzoudis A, Jakubowski JM, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Llamas-Saiz AL, Tamamis P, Mitraki A. A Novel Amyloid Designable Scaffold and Potential Inhibitor Inspired by GAIIG of Amyloid Beta and the HIV-1 V3 loop. FEBS Lett. 2018. 592, 1777–1788

 

20.  Jin UH, Park H, Li X, Davidson LA, Allred C, Patil B, Jayaprakasha G, Orr AA, Mao L, Chapkin RS, Jayaraman A, Tamamis P, Safe S. Structure-Dependent Modulation of Aryl Hydrocarbon Receptor-Mediated Activities by Flavones. Toxicological Sciences, 2018,164: 205-217.

 

21. Orr AA, Shaykhalishahi H, Mirecka EA, Jonnalagadda SVR, Hoyer W, Tamamis P*. Elucidating the Multi-Targeted Anti-Amyloid Activity and Enhanced Islet Amyloid Polypeptide Binding of β-wrapins. Computers & Chemical Engineering, 2018. https://doi.org/10.1016/j.compchemeng.2018.02.013

 

22. Orr AA, Jayaraman A, Tamamis P. Molecular Modeling of Chemoreceptor: Ligand Interactions. Methods in Molecular Biology, 2018, 1729:353-372.

 

23. Orr AA, Gonzalez-Rivera JC, Wilson M, Bhikha PR, Wang D, Contreras LM, Tamamis P. A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins. Methods, 2018, https://doi.org/10.1016/j.ymeth.2018.01.015

 

24. Jonnalagadda SVR, Ornithopoulou E, Orr AA, Mossou E, Forsyth E, Mitchell EP, Bowler MW, Mitraki A, Tamamis P. Computational Design of Amyloid Self-Assembling Peptides Bearing Aromatic Residues and the Cell Adhesive Motif Arg-Gly-Asp. Molecular Systems Design & Engineering, 2017, 2(3): 321-335.

 

25. Orr AA, Wördehoff MM. Hoyer W, Tamamis P. Uncovering the Binding and Specificity of β-Wrapins for Amyloid-β and α-Synuclein. Journal of Physical Chemistry B, 2016, 120 (50): 12781–12794.

 

26. Deidda G, Jonnalagadda SVR, Spies JW, Ranella A, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Tamamis P, Mitraki A.  Self-assembled amyloid peptides with Arg-Gly-Asp (RGD) motifs as scaffolds for tissue engineering. ACS Biomaterials Science & Engineering, 2017, 3(7): 1404–1416.

 

27. Cheng Y, Jin UH, Davidson LA, Chapkin RS, Jayaraman A, Tamamis P, Orr A, Allred C, Denison MS, Soshilov A, Weaver E, Safe S. Microbial-Derived 1,4-Dihydroxy-2-naphthoic Acid and Related Compounds as Aryl Hydrocarbon Receptor Agonists/Antagonists: Structure-Activity Relationships and Receptor Modeling. Toxicological Sciences, 2017, 155 (2): 458-473.

 

28. Khoury GA, Smadbeck J, Kieslich CA, Koskosidis AJ, Guzman YA, Tamamis P, Floudas CA.  Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment. Proteins 2017, 85(6):1078-1098.

 

29. Kieslich CA, Tamamis P, Guzman YA, Onel M, Floudas CA. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism. PLoS One. 2016, 11(2): e0148974.

 

 

Publications from Dr. Tamamis’ graduate and postgraduate studies

30. Gorham RD Jr, Forest DL, Khoury GA, Beecher CN, Tamamis P, Archontis G, Larive CK, Floudas C A, Radeke M J, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. Journal of Medicinal Chemistry, 2015, 58(2): 814-826.

 

31. Tamamis P, Floudas CA. Elucidating a Key Anti-HIV-1 and Cancer-Associated Axis: The Structure of CCL5 (Rantes) in Complex with CCR5. Scientific Reports, 2014, 4: 5447.

 

32. Tamamis P, Floudas CA. Elucidating a Key Component of Cancer Metastasis: CXCL12 (SDF-1α) Binding to CXCR4. Journal of Chemical Information and Modeling, 2014, 54 (4): 1174-1188.

 

33. Tamamis P, Floudas CA. Molecular Recognition of CCR5 by an HIV-1 gp120 V3 Loop. PLoS ONE 2014, 9 (4): e95767.

 

34. Tamamis P, Terzaki, K, Kassinopoulos M, Mastrogiannis L,  Mossou E,  Forsyth VT, Mitchell EP,  Mitraki A,  Archontis G. Self-Assembly of an Aspartate-Rich Sequence from the Adenovirus Fibre Shaft: Insights from Molecular Dynamics Simulations and Experiments. Journal of Physical Chemistry B, 2014, 118 (7): 1765-1774.

 

35. Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the Compstatin Family. ACS Synthetic Biology, 2014, 3(12): 855–869.

 

36. Khoury GA, Tamamis P, Pinnaduwage N, Smadbeck J, Kieslich CA, Floudas CA. Princeton_TIGRESS: Protein geometry refinement using simulations and support vector machines. Proteins, 2014, 82 (5): 794-814.

 

37. Tamamis P, Kasotakis E,  Archontis G, Mitraki A. Combination of Theoretical and Experimental Approaches for the Design and Study of Fibril-forming Peptides. In Protein Design: Methods and Applications. Methods in Molecular Biology, 2014, 1216: 53-70.

 

38. Tamamis P, Kieslich CA, Nikiforovich GV, Woodruff TM, Morikis D, Archontis G. Insights into the Mechanism of C5aR Inhibition by PMX53 via Implicit Solvent Molecular Dynamics Simulations and Docking. BMC Biophysics, 2014, 7: 5.

 

39. Gorham RD Jr, Forest DL, Tamamis P, López de Victoria A, Kraszni  M, Kieslich CA, Banna CD, Bellows-Peterson ML, Larive CK, Floudas CA, Archontis G, Johnson LV, Morikis D. Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Experimental Eye Research, 2013, 116: 96-108.

 

40. Tamamis P, Floudas CA. Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop. Biophysical Journal, 2013, 105 (6): 1502-1514.

 

41. Lopez de Victoria, A, Tamamis P, Kieslich, CA, Morikis, D. Insights into the Structure, Correlated Motions, and Electrostatic Properties of two HIV-1 gp120 V3 loops. PLoS ONE 2012, 7 (11): e49925.

 

42. Kieslich CA, Tamamis P, Gorham RD Jr, Lopez de Victoria A, Sausman N, Archontis G, Morikis D. Exploring protein-protein and protein-ligand interactions in the immune system using molecular dynamics and continuum electrostatics. Current Physical Chemistry 2012, 2 (4): 324-343.

 

43. Tamamis P, Lopez de Victoria A, Gorham RD, Bellows-Peterson ML, Pierou P, Floudas CA, Morikis D, Archontis G. Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs. Chemical Biology & Drug Design 2012, 79 (5): 703-718.

 

44. Tamamis P, Pierou P, Mytidou C, Floudas CA, Morikis D, Archontis G. Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin. Proteins, 2011, 79 (11): 3166-3179.

 

45. Pieridou G, Avgousti-Menelaou C, Tamamis P, Archontis G, Hayes SC. UV Resonance Raman Study of TTR(105-115) Structural Evolution as a Function of Temperature. Journal of Physical Chemistry B, 2011, 115 (14): 4088-4098.

 

46. Tamamis P, Archontis G. Amyloid-like Self-Assembly of a Dodecapeptide Sequence from the Adenovirus Fiber Shaft: Perspectives from Molecular Dynamics Simulations. Journal of Non-Crystalline Solids, 2011, 357 (2): 717-722.

 

47. Tamamis P, Morikis D, Floudas CA, Archontis G. Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins, 2010, 78 (12): 2655-2667.

 

48. Tamamis P, Kasotakis E, Mitraki A, Archontis G. Amyloid-like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations. Journal of Physical Chemistry B, 2009, 113 (47): 15639-15647.

 

49. Tamamis P, Adler-Abramovich L, Reches M, Marshall K, Sikorski P, Serpell L, Gazit E, Archontis G. Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations. Biophysical Journal, 2009, 96 (12): 5020-5029.

 

 

 

Funding

Tamamis lab has received support from:

- the National Institutes for Health,

Ø National Institute on Aging

Computational Design of Novel β-wrapins Targeting and Sequestering Amyloid-β, α-synuclein and IAPP

Ø National Institute of Environmental Health Sciences

Comprehensive Tools and Models for Addressing Exposure to Mixtures During Environmental Emergency-Related Contamination Events

 

- the National Science Foundation

Ø URoL: Epigenetics 1: Collaborative Research: Novel epitransciptomics tools to understand and modulate interactions of modified RNAs with protein readers and erasers

 

In addition, Tamamis lab has received support (startup funding, seed funding and T3 funding) from Texas A&M University andTexas A&M engineering experiment station.