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
Department of Chemical Engineering
Lab Office: 330 GERB,
Teaching Office: 225 JEB
3122 TAMU, College Station,
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.
• Tamamis lab received funding from the
NSF, on the study of RNA modifications with key protein readers and erasers.
Orr (5th year PhD student)
Ozguney (1st year PhD student)
Aswin Hanagal (1st year PhD student)
Joshua Griffith (4th year
Hannah Strong (3rd year
Our Current Research
Engineering peptide fibril-forming materials
with applications in biomedicine, energy and environment
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
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.
peptide scaffolds coordinate with alzheimer's
disease drugs. US Patent 62, 757, 384, 2018.
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.
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,
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.
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,
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:
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,
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. Self‐Assembling 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,
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.
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,
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:
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
AA, Jayaraman A, Tamamis P. Molecular Modeling of Chemoreceptor:
Ligand Interactions. Methods in Molecular Biology, 2018, 1729:353-372.
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.
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):
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):
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.
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
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.
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,
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.
P, Floudas CA. Molecular
Recognition of CCR5 by an HIV-1 gp120 V3 Loop. PLoS
ONE 2014, 9 (4): e95767.
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.
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.
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.
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.
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.
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.
P, Floudas CA. Molecular
Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop. Biophysical
Journal, 2013, 105 (6): 1502-1514.
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.
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.
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):
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.
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.
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.
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.