Phanourios Tamamis Lab

Department of Chemical Engineering

Texas A&M University

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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, and lead to the discovery of novel biomaterials and therapeutics.

 

Through the development of novel multidisciplinary computational strategies, combining biophysical-chemistry and engineering principles, our research aims at:

 

• Designing novel biomaterials with advanced applications, and understanding peptide/protein self-assembly at the atomic and molecular level;

• Elucidating how compounds or proteins can serve as inhibitors or disassemblers of peptide/protein amyloid self-assembly associated with amyloid diseases including diabetes, Alzheimer’s and Parkinson’s and designing novel compounds or proteins that can serve as therapeutics for amyloid diseases;

• Understanding biomolecular interactions between small chemical compounds, proteins and RNAs involved in key biological systems such as bacteria proteins and shedding light into key biological axes.

 

Phanourios Tamamis

 

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Assistant Professor

 

Artie McFerrin Department of Chemical Engineering

 

Texas A&M University

 

330, Giesecke Engineering Research Building

 

225, Jack E. Brown Chemical Engineering Building

 

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, a notable student of Martin Karplus (Nobel Prize in Chemistry, 2013). 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.

 

News

• Phanourios Tamamis presents our lab’s pioneering computational protocol for the design of functional amyloid materials in two conferences:

-        PEPMAT 2018, London, UK, July 16-18, 2018.

-        Current Challenges in Amyloid Diseases: ​From Molecular Mechanisms ​to the Cell and Clinics, Ein Bokek, Israel, September 2-6, 2018.

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• Sai Vamshi Jonnalagadda, Asuka Orr, Kendal Henderson, and Chang-Hyun Choi from Tamamis lab, in collaboration with several experimental labs including Dr. Mitraki’s and Dr. Jeong’s labs, published a paper on the first computational design protocol to functionalize amyloid materials binding to ions.  The paper was accepted in J. Phys. Chem. B

Amyloid materials are gaining increasing attention as promising materials for applications in numerous fields. Computational methods have been successfully implemented to investigate the structures of short amyloid-forming peptides, yet their application in the design of functional amyloid materials is still elusive. Here, we developed a computational protocol for the design of functional amyloid materials capable of binding to an ion of interest. We applied the protocol in a test case involving the design of amyloid materials with cesium ion deposition and capture properties. As part of the protocol, we used an optimization-based design model to introduce mutations at non-β-sheet residue positions of an amyloid designable scaffold. The designed amino acids introduced to the scaffold mimic how amino acids bind to cesium ions according to experimentally resolved structures, and also aim to energetically stabilize the bound conformation of the pockets. The optimum designs were computationally validated using a series of simulations and structural analysis to select the top designed peptides predicted to form fibrils with cesium ion binding properties for experimental testing. Experiments verified the amyloid-forming properties of the selected top designed peptides, as well as the cesium ion deposition and capture properties by the amyloid materials formed. This study demonstrates the first, to the best of our knowledge, computational design protocol to functionalize amyloid materials and suggests that its further advancement can lead to novel highly promising functional amyloid materials of the future.

 

Previous Key Stories from 2018

 

• Sai Vamshi Jonnalagadda, Asuka Orr and Joseph Jakubowski from Tamamis lab, in collaboration with Dr. Mitraki’s lab and several other labs in Europe published paper on a novel amyloid designable scaffold and potential inhibitor inspired by GAIIG of amyloid beta and the HIV-1 V3 loop. 

 

• Phanourios Tamamis received 2018 KANEKA Junior Faculty Award for outstanding performance and dedication in his research, recognized by the Polymer Technology Center of the Texas A&M Engineering Experiment Station and the Kaneka Foundation.  

 

• Asuka Orr and Leevin Mao from Tamamis lab, in collaboration with Dr. Stephen Safe’s lab, published a paper on the structure-dependent modulation of aryl hydrocarbon receptor-mediated activities by flavones.  

 

• Asuka Orr and Sai Vamshi R. Jonnalagadda from Tamamis lab, in collaboration with Wolfgang Hoyer’s lab, published a paper on elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding of β-wrapins.  

 

Asuka Orr and Mark Wilson from Tamamis lab, in collaboration with Lydia A. Contreras lab, published a paper on the first high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins.  

 

Asuka Orr from Tamamis lab, in collaboration with Arul Jayaraman, published a paper on molecular modeling of chemoreceptor:ligand Interactions.  

 

• Tamamis lab receives funding from the National Institute on Aging (NIH) to design novel β-wrapins as potential therapeutics for Alzheimer’s, Parkinson’s and diabetes type 2 diseases.

 

Previous Key Stories from 2017

 

• Graduate students Vamshi Jonnalagadda and Asuka Orr gave three presentations at the AIChE meeting in Minneapolis.

https://aiche.confex.com/aiche/2017/meetingapp.cgi/Paper/500283

https://aiche.confex.com/aiche/2017/meetingapp.cgi/Paper/499813

https://aiche.confex.com/aiche/2017/meetingapp.cgi/Paper/501471

 

       

 

A new Ph.D. student, Joseph Jakubowski, joined Tamamis lab.

 

Tamamis lab received a Seed Grant for Water Research from the Texas A&M Engineering Experiment Station.

 

Lab Members

 

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Sai Vamshi Jonnalagadda

4th year Ph.D. student

Asuka Orr

3rd year Ph.D. student

Joseph Jakubowski

2nd year Ph.D. student

 

 

 

 

 

 

 

Alexis Coley 

4th Year Undergrad.

 Kendal Henderson

4th Year Undergrad.

Brendan Woodcock

3rd Year Undergrad.

Doan Le

3rd Year Undergrad.

 

 

 

 

 

Sarah Kuhlmann

3rd Year Undergrad.

Savannah Cooper

3rd Year Undergrad.

Patricia Barreto

3rd Year Undergrad.

 

 

 

 

Research

Our Current Research Directions

Engineering novel peptide self-assembled bio-nanomaterials with promising applications in biomedicine, energy and environment

Computational methods possess the capacity to provide atomic-level insights into the β-sheet structural organization of amyloid-forming self-assembled peptides, and peptide-based nanostructures. Our research aims at exploiting the self-assembly properties of β-sheet or α-helical peptides/proteins to engineer novel peptide self-assembled biological nanomaterials with promising applications in biomedicine, energy and environment.

 

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 amyloidogenic peptides and proteins, and (ii) designing protein and non-proteins-based inhibitors or disassemblers of amyloid formation, as potential therapeutics for amyloid diseases, including Alzheimer’s, Parkinson’s and diabetes diseases. 

 

Elucidating the biomolecular complex structures of small-molecule ligand : protein and RNA : proteins complexes, shedding light into key biological axes and discovering novel potential therapeutics.

Understanding the binding of small ligands to proteins or RNAs to proteins 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 the molecular recognition of proteins (e.g., in bacteria proteins) by small-molecule ligands or RNAs. We emphasize on developing novel computational tools to elucidate the structures and interactions formed between small-molecule ligands and proteins or between chemically modified RNAs and proteins. 

 

 

Patents

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

 

Publications

Peer-Reviewed Papers and Book Chapters

Publications from Tamamis lab

 

1. 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.

 

2. 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.

 

3. 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.

 

4. 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

 

5.  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.

 

6. 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

 

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

 

8. 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

 

9. 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.

 

10. 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.

 

11. 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.

G. Deidda and S.V.R. Jonnalagadda were equally contributing first authors

 

12. 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.

 

13. 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.

 

14. 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

15. 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.

 

16. 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.

 

17. 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.

 

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

 

19. 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.

 

20. 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.

 

21. 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.

 

22. 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.

 

23. 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.

 

24. 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.

 

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

 

26. 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.

 

27. 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.

 

28. 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.

 

29. 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.

 

30. 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.

 

31. 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.

 

32. 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.

 

33. 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.

 

34. 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.

 

 

 

Alumni

 

 

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Yeonsu Kwak

Ex-Master’s Student

(Graduated in June 2016)

 

Mark Wilson

Ex-Master’s Student

 

 

 

 

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Harry MacTough

Ex-Undergraduate Researcher

Jacob Spies

Ex-Undergraduate Researcher

Andrew Palughi

Ex-Undergraduate Researcher – Graduate Student at Texas A&M University

 

 

 

 

 

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   Chang-Hyun Choi

Ex-Undergraduate Researcher – Graduate Student at Princeton University

Kate Helms

Ex-Undergraduate Researcher

Jenny Nacu

Ex-Undergraduate Researcher

 

 

Alexandra Koskosidis

Ex-High-School Researcher undergrad. at Princeton University

Danielle Scott

Ex-Undergraduate Researcher

Leevin Mao

Ex-Undergraduate Researcher

 

 

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