Publications

(78) Santiago, T.; Konstantinovsky, D.; Tremblay, M.; Perets, E.; Hammes-Schiffer, S.; Yan, E. C. Y. “Drug binding disrupts chiral water structures in the DNA first hydration shell” Chem. Sci. 16, 6853, 2025.

(77) Perets, E.; Santiago, T.; Neu, J.; Yan, E. C. Y. “Water-protein interactions as a driver of phase separation, biology, and disease” Biophys. J. 123, 3859, 2024.

(76) Perets, E.; Konstantinovsky, D.; Santiago, T.; Videla, P.; Tremblay, M.; Velarde, L.; Batista, V.; Hammes-Schiffer, S.; Yan, E. C. Y. “Beyond the “Spine of Hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures” J. Chem. Phys. 161, 095104, 2024.

(75) Konstantinovsky, D.; Santiago, T.; Tremblay, M.; Simpson, G. J.; Hammes-Schiffer, S.; Yan, E. C. Y. “Theoretical basis for interpreting heterodyne chirality-selective sum frequency generation spectra of water” J. Chem. Phys. 160, 055102, 2024.

(74) Konstantinovsky, D.; Yan, E. C. Y.; Hammes-Schiffer, S. “Characterizing Interfaces by Voronoi Tessellation” J. Phys. Chem. Lett. 14, 5260, 2023.

(73) Yan, E. C. Y.; Perets, E. A.; Konstantinovsky, D.; Hammes-Schiffer, S. “Detecting Interplay of Chirality, Water, and Interfaces for Elucidating Biological Functions” Acc. Chem. Res. 56, 12, 1494, 2023.

(72) Konstantinovsky, D.; Perets, E. A.; Santiago, T.; Olesen, K.; Wang, Z.; Soudackov, A., V,; Yan, E. C. Y.; Hammes-Schiffer, S. “Design of an Electrostatic Frequency Map for the NH Stretch of the Protein Backbone and Application to Chiral Sum Frequency Generation Spectroscopy” J. Phys. Chem. B 127, 11, 2418, 2023.

(71) Konstantinovsky, D.; Perets, E. A.; Santiago, T.; Velarde, L.; Hammes-Schiffer, S.; Yan, E. C. Y. “Detecting the First Hydration Shell Structure around Biomolecules at Interfaces” ACS Cent. Sci. 8, 10, 1404, 2022.

• Read the first reaction to the paper:
  Nagata and Bonn. “Biomolecular Chirality Is Imprinted on One Layer of Hydration Water”.

(70) Perets, E. A.; Olesen, K. B.; Yan, E. C. Y. “Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces” Langmuir 38, 5765, 2022.

(69) Konstantinovsky, D.; Perets, E. A.; Yan, E. C. Y.; Hammes-Schiffer, S. “Simulation of the Chiral Sum Frequency Generation Response of Supramolecular Structures Requires Vibrational Couplings” J. Phys. Chem. B 125, 12072, 2021.

(68) Perets, E. A.; Konstantinovsky, D.; Fu, L.; Chen, J.; Wang, H.-F.; Hammes-Schiffer, S.; Yan, E. C. Y. “Mirror-image antiparallel β-sheets organize water molecules into superstructures of opposite chirality” Proc. Natl. Acad. Sci. 117, 32902, 2020.

• Read the commentary:
  Pullanchery and Roke. “Handy water: Chiral superstructures around peptide β-sheets”.

(67) Perets, E. A.; Chabeda, D.; Gong, A. Z.; Huang, X.; Fung, T. S.; Ng, K. Y.; Bathgate, M.; Yan, E. C. Y. “Impact of the Emergency Transition to Remote Teaching on Student Engagement in a Non-STEM Undergraduate Chemistry Course in the Time of COVID-19” J. Chem. Educ. 97, 2439, 2020.

(66) Perets, E. A.; Videla, P. E.; Yan, E. C. Y.; Batista, V. S. “Chiral Inversion of Amino Acids in Anti-Parallel β-sheets Probed by Vibrational Sum Frequency Generation Spectroscopy” J. Phys. Chem. B 123, 5769, 2019.

(65) Perets, E. A.; Yan, E. C. Y. “Chiral Water Superstructures Around Anti-Parallel β-sheets Observed by Chiral Vibrational Sum Frequency Generation Spectroscopy” J. Phys. Chem. Lett. 10, 3395, 2019.

(64) Liu, W.; Fu, L.; Wang, Z.; Sohrabpour, Z.; Li, X.; Liu, Y.; Wang, H.-F.; Yan, E. C. Y. “Two dimensional crowding effects on protein folding at interfaces observed by chiral vibrational sum frequency generation spectroscopy” Phys. Chem. Chem. Phys. 20, 22421, 2018.

(63) Culhane, K. J.; Belina, M. E.; Sims, J. N.; Cai, Y.; Liu, Y.; Wang, P. S. P.; Yan, E. C. Y. “Parathyroid Hormone Senses Extracellular Calcium to Modulate Endocrine Signaling upon Binding to the Family B GPCR Parathyroid Hormone 1 Receptor” ACS Chem. Biol. 13, 2347, 2018.

(62) Kaufman, G.; Liu, W.; Williams, D. M.; Choo, Y.; Gopinadhan, M.; Samudrala, N.; Sarfati, R.; Yan, E. C. Y.; Regan, L.; Osuji, C. “Flat Drops, Elastic Sheets, and Microcapsules by Interfacial Assembly of a Bacterial Biofilm Protein, BslA” Langmuir 33, 13590, 2017.

(61) Szundi, I.; Funatogawa, C.; Guo, Y.; Yan, E. C. Y.; Kliger, D. S. “Protein Sequence and Membrane Lipid Roles in the Acitivation Kinetics of Bovine and Human Rhodopsins” Biophys. J. 113, 1934, 2017.

(60) Liu, W.; Li, S.; Wang, Z.; Yan, E. C. Y.; Leblanc, R. M. “Characterization of surface-active biofilm protein BslA in self-assembling monolayer at the air-water interface” Langmuir 33, 7548, 2017.

(59) Cai, Y.; Liu, Y.; Culhane, K.J.; DeVree, B. T.; Yang, Y.; Sunahara, R. K.; Yan, E. C. Y. “Purification of family B G protein-coupled receptors using nanodiscs: Application to human glucagon-like peptide-1 receptor” PLOS ONE 12, e0179568, 2017.

(58) Perets, E. A.; Yan, E. C. Y. “The H₂O Helix: The Chiral Water Superstructure Surrounding DNA” ACS Cent. Sci. 3, 683, 2017.

(57) Guo, Y.; Hendrickson, H. P.; Videla, P. E.; Chen, Y.-N.; Ho, J.; Sekharan, S.; Batista, V. S.; Tully, J. C.; Yan, E. C. Y. “Probing the remarkable thermal kinetics of visual rhodopsin with E181Q and S186A mutants” J. Chem. Phys. 146, 215104, 2017.

(56) Serebryany, E.; Folta-Stogniew, E.; Liu, J.; Yan, E. C. Y. “Homodimerization enhances both sensitivity and dynamic range of the ligand-binding domain of type 1 metabotropic glutamate receptor” FEBS Letters 590, 4308, 2016.

(55) Schloss, A.; Liu, W.; Williams, D. M.; Kaufman, G.; Hendrickson, H. P.; Rudshteyn, B.; Fu, L.; Wang, H.; Batista, V. S.; Osuji, C.; Yan, E. C. Y.; Regan, L.; “Fabrication of Modularly Functionalizable Microcapsules Using Protein-Based Technologies” ACS Biomater. Sci. Eng. 2, 1856, 2016.

(54) Singhal, A.; Guo, Y.; Matkovic, M.; Schertler, G.; Deupi, X.; Yan, E. C. Y.; Standfuss, J. “Structural role of the T94I rhodopsin mutation in congenital stationary night blindness” EMBO reports 17, 1237, 2016.

(53) Wang, Z.; Morales-Acosta, M. D.; Li, S.; Liu, W.; Kanai, T.; Liu, Y.; Chen, Y. N.; Walker, F. J.; Ahn, C.; Leblanc, R. M.; Yan, E. C. Y. “A Narrow Amide I Vibrational Band Observed by Sum Frequency Generation Spectroscopy Reveals Highly Ordered Structures of a Biofilm Protein at the Air/Water Interface” Chem. Comm. 52, 2956, 2016.

(52) Fu, L.; Wang, Z.; Batista, V. S.; Yan, E. C. Y. “New Insights from Sum Frequency Generation Vibrational Spectroscopy into the Interactions of Islet Amyloid Polypeptides with Lipid Membranes” J. Diabetes Res. 612051, 2015.

(51) Culhane, K. J.; Liu, Y.; Cai, Y.; Yan, E. C. Y. “Transmembrane signal transduction by peptide hormones via family B G protein-coupled receptors” Front. Pharmacol. 6, 264, 2015.

(50) Wang, Z.; Fu, L.; Ma, G.; Yan, E. C. Y. “Broad-Bandwidth Chiral Sum Frequency Generation Spectroscopy for Probing the Kinetics of Proteins at Interfaces” Langmuir 31, 11384, 2015.

(49) Fu, L.; Wang, Z.; Psciuk, T. B.; Xiao, D.; Batista, V. S.; Yan, E. C. Y. “Characterization of Parallel β-Sheets at Interfaces by Chiral Sum Frequency Generation Spectroscopy” J. Phys. Chem. Lett. 6, 1310, 2015.

(48) Liu, Y.; Cai, Y.; Liu, W.; Li, X. H.; Rhoades, E.; Yan, E. C. Y. “Triblock Peptide-Linker-Lipid Molecular Design Improves Potency of Peptide Ligands Targeting Family B G Protein-Coupled Receptors” Chem. Comm. 51, 6157, 2015.

(47) Yan, E. C. Y.; Wang, Z.; Fu, L. “Proteins at Interfaces Probed by Chiral Sum Frequency Generation Spectroscopy” J. Phys. Chem. B 119, 2769, 2015.

(46) Mooney, V.; Skharan, S.; Liu, J.; Guo, Y.; Batista, V. S.; Yan, E. C. Y. “Kinetics of Thermal Activation of an Ultraviolet Cone Pigment” J. Am. Chem. Soc. 137, 307, 2015.

(45) Guo, Y.; Skharan, S.; Liu, J.; Batista, V. S.; Tully, J. C.; Yan, E. C. Y. “Unusual kinetics of thermal decay of dim-light photoreceptors in vertebrate vision” Proc. Natl. Acad. Sci. U.S.A. 108, 26111, 2014.

(44) Fu, L.; Wang, Z.; Yan, E. C. Y. “N-H Stretching Modes Around 3300 Wavenumber From Peptide Backbones Observed by Chiral Sum Frequency Generation Vibrational Spectroscopy” Chirality 22, 306, 2014.

(43) Yan, E. C. Y.; Fu, L.; Wang, Z.; Liu, W. “Biological Macromolecules at Interfaces Probed by Chiral Sum Frequency Generation Spectroscopy” Special Thematic Issue: Aqueous Interfaces” Chem. Rev. 114, 8471, 2014.

(42) Sekharan, S.; Mooney, V.; Rivalta, I.; Kazmi, M. A.; Neitz, M.; Neitz, J.; Sakmar, T. P.; Yan, E. C. Y., Batista, V. B. “Spectral Tuning of Ultraviolet Cone Pigments: An Interhelical Lock Mechanism” J. Am. Chem. Soc. 135, 19064, 2013.

(41) Liu, W.; Wang, Z.; Fu, L.; Leblanc, R. M.; Yan, E. C. Y. “Lipid Compositions Modulate Fluidity and Stability of Bilayers: Characterization by Surface Pressure and Sum Frequency Generation Spectroscopy” Langmuir 29, 15022, 2013.

(40) Guo, Y.; Young, K.; Yan, E. C. Y. Book Chapter: “Guided Inquiry and Project-Based Learning in Biophysical Spectroscopy” in Teaching Bioanalytical Chemistry, Edited by Harvey J. M. Hou, ACS Books, Chapter 13, p261-291, 2013.

(39) Liu, M. Y.; Liu, J.; Mehrotra, D.; Liu, Y.; Guo, Y.; Baldera-Aguayo, P. A.; Mooney, V.; Nour, A. M.; Yan, E. C. Y. “Thermal Stability of Rhodopsin and Progression of Retinitis Pigmentosa: A Comparison of S186W and D190N Rhodopsin Mutants” J. Biol. Chem. 288, 17698, 2013.

(38) Wang, Z.; Fu, L.; Yan, E. C. Y. “C–H Stretch for Probing Kinetics of Self-Assembly into Macromolecular Chiral Structures at Interfaces by Chiral Sum Frequency Generation Spectroscopy” Langmuir 29, 4077, 2013.

(37) Fu, L.; Xiao, D. Q.; Wang, Z.; Batista, V. S.; Yan, E. C. Y. “Chiral Sum Frequency Generation for In Situ Probing Proton Exchange in Antiparallel β-Sheets at Interfaces” J. Am. Chem. Soc. 135, 3592, 2013.

(36) Mitra, N.; Liu, Y.; Liu, J.; Serebryany, E.; Mooney, V.; DeVree, B. T.; Sunahara, R. K.; Yan, E. C. Y. “Calcium-Dependent Ligand Binding and G-protein Signaling of Family B GPCR Parathyroid Hormone 1 Receptor Purified in Nanodiscs” ACS Chem. Biol. 8, 617, 2013.

(35) Zhu, G. A.; Serebryany, E.; Yan, E. C. Y. “Rational Design of Supramolecular Lipid/Detergent Assemblies for Purification of G Protein-Coupled Receptors” Invited Submission, Encyclopedia of Supramolecular Chemistry, 2012.

(34) Mooney, V.; Szundi, I.; Lewis, J. W.; Yan, E. C. Y.; Kliger, D. S. “Schiff Base Protonation Changes in Siberian Hamster Ultraviolet Cone Pigment Photointermediates” Biochem. 51, 2630, 2012.

(33) You, Y. M.; Bloomfield, A.; Liu, J.; Fu, L.; Herzon, S.; Yan, E. C. Y. “Real-Time Kinetics of Surfactant Molecules Transfer between Emulsion Particles Probed by In Situ Second Harmonic Generation Spectroscopy” J. Am. Chem. Soc. 134, 4264, 2012.

(32) Xiao, D. Q.; Fu, L.; Liu, J.; Batista, V. S.; Yan, E. C. Y. “Effects of Bilayer Surface Charge Density on Molecular Adsorption and Transport across Liposome Bilayers” J. Mol. Biol. 421, 537, 2012.

(31) Serebryany, E.; Zhu, G. A.; Yan, E. C. Y. “Artificial membrane-like environments for in vitro studies of purified G-protein coupled receptors” Invited Review, BBA-Biomembrane 1818, 225, 2012.

(30) Fu, L.; Wang, Z.; Yan, E. C. Y. “Chiral Vibrational Structures of Proteins at Interfaces Probed by Sum Frequency Generation Spectroscopy” Invited Submission, Special Issue: Applications of Circular Dichroism, Int. J. Mol. Sci. 12, 9404, 2011.

(29) Liu, J; Liu, M. Y.; Fu, L.; Zhu, G. A.; Yan, E. C. Y. “Chemical Kinetic Analysis of Thermal Decay of Rhodopsin Reveals Unusual Energetics of Thermal Isomerization and Hydrolysis of Schiff Base” J. Biol. Chem. 286, 38408, 2011.

(28) Liu, J.; Liu, M. Y.; Mooney, V.; Bhagat, A.; Nguyen, J.; Yan, E. C. Y. “Thermal Properties of Rhodopsin: Insight into Molecular Mechanism of Dim-Light Vision” J. Biol. Chem. 286, 27622, 2011.

(27) Fu, L.; Liu, J.; Yan, E. C. Y. “Chiral Sum Frequency Generation Spectroscopy for Characterizing Protein Secondary Structures at Interfaces” J. Am. Chem. Soc. 133, 8094, 2011.

(26) Wu, W. T.; Mitra, N.; Yan, E. C. Y.; Zhou, S. Q. “Multifunctional Hybrid Nanogel for Integration of Optical Glucose Sensing and Self-Regulated Insulin Release at Physiological pH” ACS Nano 4, 4831, 2010.

(25) Fu, L.; Ma, G.; Yan, E. C. Y. “In Situ Misfolding of Human Islet Amyloid Polypeptide at Interfaces Probed by Sum Frequency Generation” J. Am. Chem. Soc. 132, 5405, 2010.

(24) Durrell, A. C; Gary, H. B.; Hazari, N.; Incarvito, C. D.; Liu, J.; Yan, E. C. Y. “Tris (hydroxypropyl) phosphine Oxide: A Chiral Three-Dimensional Material with Non-linear Optical Properties” Cryst. Growth Des. 10, 1482, 2010.

(23) Liu, J.; Liu, M. Y.; Nguyen,J. B.; Bhagat, A.; Mooney, V.; Yan, E. C. Y. “Thermal Decay of Rhodopsin Involves both Thermal Isomerization of 11-cis Retinal in the Retinal Binding Site and Hydrolysis of Schiff Base.”  J. Am. Chem. Soc. 131, 8750, 2009.

(22) Ma, G; Liu, J.; Fu, L.; Yan, E. C. Y. “Probing Water and Biomolecules at the Air/Water Interface with a Broad-Bandwidth Vibrational Sum Frequency Generation Spectrometer from 3800 to 900 cm^-1” Appl. Spectro. 63, 528. 2009.

Publications prior to Yale

(21) Ahuja, S.; Eilers, M.; Hirshfeld, A.; Yan, E. C. Y.; Ziliox, M.; Sakmar, T. P.; Sheves, M.; Smith, S. O. “6-s-cis Conformation and Polar Binding Pocket of the Retinal Chromophore in the Photoactivated State of Rhodopsin” J. Am. Chem. Soc.131, 15160, 2009.

(20) Ahuja, S.; Hornak, V.; Yan, E. C. Y.; Syrett, N.; Goncalves, J. A.; Hirshfeld, A.; Ziliox, M.; Sakmar, T. P.; Sheves, M.; Reeves, P.J.; Smith, S. O. & Eilers, M. “Helix Movement is Coupled to Displacement of Extracellular Loop 2 in Rhodopsin Activation.” Nat. Struct. Mol. Biol.16, 168. 2009.

(19) Ye, S. X.; Köhrer, C.; Huber, T.; Kazmi, M.; Sachdev, P.; Yan, E. C. Y.; Bhagat, A.; RajBhandary, U. L.; Sakmar, T. P. “Site-specific Incorporation of Keto Amino Acids Into Functional G Protein-Coupled Receptors Using Unnatural Amino Acid Mutagenesis” J. Biol. Chem. 283, 1525, 2008.

(18) Yan, E. C. Y.; Epps, J.; Lewis, J. W.; Szundi, I; Bhagat, A.; Sakmar, T. P.; Kliger, D. S. “Photointermediates of the Rhodopsin S186A Mutant as a Probe of the Hydrogen Bond Network in the Chromophore Pocket and Counterion Switch” Invited Paper, J. Phy. Chem. C. 111, 8843, 2007.

(17) Vogel, R.; Siebert, F; Yan, E. C. Y.; Sakmar, T. P.; Hirshfeld, A.; Sheves, M. “Modulating Rhodopsin Receptor Activation by Altering the pKa of the Retinal Schiff Base” J. Am. Chem. Soc. 128, 10503, 2006.

(16) Ludeke, S; Beck, R.; Yan, E. C. Y.; Sakmar, T. P.; Siebert, F.; Vogel, R. “The Role of Glu181 in the Photoactivation of Rhodopsin”  J. Mol. Biol.  353, 245, 2005.

(15) Yan, E. C. Y.; Ganim, Z.; Kazmi, M. A.; Chang, B. S. W.; Sakmar, T. P.; Mathies, R. A. “Resonance Raman Analysis of the Mechanism of Energy Storage and Chromophore Distortion in the Primary Visual Photoproduct” Biochemistry 43, 10867, 2004.

(14) Yan, E. C. Y.; Kazmi, M.A.; Ganim, Z.; Hou, J. M.; Pan, D. H.; Chang, B. S. W.; Sakmar, T. P.; Mathies, R. A  “Retinal counterion Switch in the Photoactivation of G Protein-Coupled Receptor Rhodopsin” Proc. Natl. Acad. Sci. U.S.A. 100, 9262, 2003.

• Commentary by Birge, R. R. and Knox, B. E. “Perspectives on the counterion switch-induced photoactivation of the G protein-coupled receptor rhodopsin” Proc. Natl. Acad. Sci. U.S.A. 100, 9105, 2003.

(13) Yan, E. C. Y.; Kazmi, M. A.; De, S.; Chang, B. S. W.; Seibert, C.; Marin, E. P.; Mathies, R. A.; Sakmar, T. P. “Function of Extracellular Loop 2 in Bovine Rhodopsin: Glutamic Acid 181 Modulates Stability and Wavelength Maximal Absorption of Metarhodopsin II” Biochemistry 41, 3620, 2002.

(12) Shang, X. M.; Liu, Y.; Yan, E. C. Y.; Eisenthal, K. B. “Effect of Counterions on Molecular Transport across Liposome Bilayer: Probed by Second Harmonic Generation” J. Phys. Chem. B 105, 12816, 2001.

(11) Yan, E.C.Y.; Liu, Y.; Eisenthal, K.B. “In-situ Studies of Molecular Transfer between Colloidal Surfaces by Second Harmonic Generation” J. Phys. Chem. B 105, 8531, 2001.

(10) Liu, Y.; Yan, E. C. Y.; Zhao, X. L.; Eisenthal, K. B. “Surface Potential of Charged Liposomes Determined by Second Harmonic Generation” Langmuir 17, 2063, 2001.

(9) Liu, Y.; Yan, E. C. Y.; Eisenthal, K. B. “Effects of Bilayer Surface Charge Density on Molecular Adsorption and Transport across Liposome Bilayers” Biophys. J. 80, 1004, 2001.

(8) Yan, E. C. Y.; Eisenthal, K. B. “Effects of Cholesterol on Molecular Transport of Organic Cations across Liposome Bilayers Probed by Second Harmonic Generation” Biophys. J. 79, 898, 2000.

(7) Yan, E. C. Y.; Eisenthal, K. B. “Rotational Dynamics of Anisotropic Particles Studied by Second Harmonic Generation” J. Phys. Chem. B 104, 6686, 2000.

(6) Yan, E. C. Y.; Eisenthal, K. B. “Probing the Interface of Microscopic Clay Particles in Aqueous Solution by Second Harmonic Generation” J. Phys. Chem. B 103, 6056, 1999.

(5) Yan, E. C. Y.; Liu, Y.; Eisenthal, K. B. “New Method for Determination of Surface Potential of Microscopic Particles by Second Harmonic Generation” J. Phys. Chem. B 102, 6331, 1998.

(4) Wang, H. F.; Yan, E. C. Y.; Liu, Y.; Eisenthal, K.B. “Energetics and Population of Molecules at Microscopic Liquid and Solid Surfaces” J. Phys. Chem. 102, 4446, 1998.

(3) Wang, H. F.; Borguet, E.; Yan, E. C. Y.; Zhang, D.; Gutow, J.; Eisenthal, K. B. “Molecules at Liquid and Solid Surfaces” Langmuir 14, 1472, 1998.

(2) Wang, H. F.; Yan, E. C. Y.; Borguet, E.; Eisenthal, K. B. “Second Harmonic Generation from the Surface of Centrosymmetric Particles in Bulk Solution” Chem. Phys. Letts. 259, 15, 1996.

(1) Wu, C.; Yan, C. Y. “Studies of the Swelling and Drying Kinetics of Thin Gel Films by In-Situ Interferometry” Macromolecules 27, 4516, 1994.