Publications

*equal contribution

Preprints

1. Ahmed IA, Liu J, Gieniec KA, Bair-Marshall CJ, Adewakun AB, Hetzler BE, Arp C, Khatri L, Vanwalleghem GC, Seidenberg AT, Cowin P, Trauner D, Chao MV, Tsien RW, Davis FM, Froemke RC. “Optopharmacological tools for precise spatio-temporal control of oxytocin signaling in the central nervous system and periphery.” BioRxiv (2022). (Currently in revision for Nature Methods) PDF

Articles

2. Fong KP, Ahmed IA, Mravic M, Jo H, Kim OV, Litvinov RI, Weisel JW, DeGrado WF, Gai F, Bennett JS. “Visualization of Platelet Integrins via Two-Photon Microscopy Using Anti-transmembrane Domain Peptides Containing a Blue Fluorescent Amino Acid.” Biochemistry. (2021) Jun1;60(21):1722-1730. PDF

3. Micikas RJ*, Ahmed IA*, Acharyya A, Smith AB, Gai F. “Tuning the electronic transition energy of indole via substitution: application to identify tryptophan-based chromophores that absorb and emit visible light.” Phys Chem Chem Phys. (2021) Mar 21;23(11):6433-6437. PDF

4. Ahmed IA, Rodgers JM, Eng C, Troxler T, Gai F. “PET and FRET utility of an amino acid pair: tryptophan and 4- cyanotryptophan.” Phys Chem Chem Phys. (2019) Jun 28;21(24):12843-12849. PDF

5. Zhang K*, Ahmed IA*, Kratochvil HT, DeGrado WF, Gai F, Jo H. “Synthesis and application of the blue fluorescent amino acid l-4-cyanotryptophan to assess peptide-membrane interactions.” Chem Commun (Camb). (2019) Apr 25;55(35):5095-5098. PDF

6. Ahmed IA, Acharyya A, Eng CM, Rodgers JM, DeGrado WF, Jo H, Gai F. “4-Cyanoindole-2'-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics.” Molecules. (2019) Feb 8;24(3):602. PDF

7. Hilaire MR*, Ahmed IA*, Lin CW, Jo H, DeGrado WF, Gai F. “Blue fluorescent amino acid for biological spectroscopy and microscopy.” Proc Natl Acad Sci U S A. (2017) Jun 6;114(23):6005-6009. PDF

8. Ahmed IA, Gai F. Simple method to introduce an ester infrared probe into proteins. Protein Sci. (2017) Feb;26(2):375-381. PDF

9. Markiewicz BN, Lemmin T, Zhang W, Ahmed IA, Jo H, Fiorin G, Troxler T, DeGrado WF, Gai F. “Infrared and fluorescence assessment of the hydration status of the tryptophan gate in the influenza A M2 proton channel.” Phys Chem Chem Phys. (2016) Oct 19;18(41):28939-28950. PDF

10. Pazos IM*, Ahmed IA*, Berríos MI, Gai F. “Sensing pH via p-cyanophenylalanine fluorescence: Application to determine peptide pKa and membrane penetration kinetics.” Anal Biochem. (2015) Aug 15;483:21-6. PDF

11. Mutter AC, Norman JA, Tiedemann MT, Singh S, Sha S, Morsi S, Ahmed I, Stillman MJ, Koder RL. “Rational design of a zinc phthalocyanine binding protein.” J Struct Biol. (2014) Feb;185(2):178-85 PDF

12. Zhang L, Anderson JL, Ahmed I, Norman JA, Negron C, Mutter AC, Dutton PL, Koder RL. “Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein.” Biochemistry. (2011) Nov 29;50(47):10254-61. PDF

Reviews / Book Chapters

13. Mukherjee D*, Ahmed IA*, Gai F. “Site-specific Interrogation of Protein Structure and Stability.” Methods Mol Biol. (2022) 2376:65-87. | Book chapter in Volume 685 “New Experimental Probes for Enzyme Specificity and Mechanism” edited by John P. Richard and Graham R. Moran. PDF

14. Acharyya A*, Ahmed IA*, Gai F. “4-Cyanoindole-based fluorophores for biological spectroscopy and microscopy.” Methods Enzymol. (2020) 639:191-215. | Book chapter in Volume 639 “Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Methods for Optical Imaging and Conjugation” edited by David M. Chenoweth. PDF

DEI

15. Ahmed I, Armstrong A, Clemons TA, Clune-Taylor C, Love-Rutledge ST, Phillips MA, Rogers CD, Williams MJ. How do DEI initiatives impact STEMM, and why do we still need them? Cell (2023) 186(12):2506-2509. PDF