@article{code_qiu_solov'yov_lee_shin_roland_sagui_houde_rand_jorgensen_2023, title={Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties}, ISSN={["1520-5126"]}, DOI={10.1021/jacs.3c04068}, abstractNote={Protein glycosylation is a common post-translational modification on extracellular proteins. The conformational dynamics of several glycoproteins have been characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS). However, it is, in most cases, not possible to extract information about glycan conformation and dynamics due to the general difficulty of separating the deuterium content of the glycan from that of the peptide (in particular, for O-linked glycans). Here, we investigate whether the fragmentation of protonated glycopeptides by collision-induced dissociation (CID) can be used to determine the solution-specific deuterium content of the glycan. Central to this concept is that glycopeptides can undergo a facile loss of glycans upon CID, thereby allowing for the determination of their masses. However, an essential prerequisite is that hydrogen and deuterium (H/D) scrambling can be kept in check. Therefore, we have measured the degree of scrambling upon glycosidic bond cleavage in glycopeptides that differ in the conformational flexibility of their backbone and glycosylation pattern. Our results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. In contrast, the glycosidic bond cleavage occurs without any scrambling in the glycopeptide antibiotic vancomycin, reflecting that the glycan cannot interact with the peptide moiety due to a conformationally restricted backbone as revealed by molecular dynamics simulations. Scrambling is also inhibited, albeit to a lesser degree, in the conformationally restricted glycopeptides ristocetin and its pseudoaglycone, demonstrating that scrambling depends on an intricate interplay between the flexibility and proximity of the glycan and the peptide backbone.}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Code, Christian and Qiu, Danwen and Solov'yov, Ilia A. and Lee, Jung-Goo and Shin, Hyeon-Cheol and Roland, Christopher and Sagui, Celeste and Houde, Damian and Rand, Kasper D. and Jorgensen, Thomas J. D.}, year={2023}, month={Oct} }
 @article{nixon_mansouri_singh_du_davis_lee_slabaugh_vandavasi_o’neill_roberts_et al._2016, title={Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex}, volume={6}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep28696}, DOI={10.1038/srep28696}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Nixon, B. Tracy and Mansouri, Katayoun and Singh, Abhishek and Du, Juan and Davis, Jonathan K. and Lee, Jung-Goo and Slabaugh, Erin and Vandavasi, Venu Gopal and O’Neill, Hugh and Roberts, Eric M. and et al.}, year={2016}, month={Jun} }
 @article{lee_sagui_roland_2010, title={Dimerization free energy of Vancomycin-group antibiotics and the cooperative effect: A density functional approach}, volume={110}, number={15}, journal={International Journal of Quantum Chemistry}, author={Lee, J. G. and Sagui, C. and Roland, C.}, year={2010}, pages={2894–2902} }
 @article{moradi_lee_babin_roland_sagui_2010, title={Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation}, volume={110}, number={15}, journal={International Journal of Quantum Chemistry}, author={Moradi, M. and Lee, J. G. and Babin, V. and Roland, C. and Sagui, C.}, year={2010}, pages={2865–2879} }
 @article{lee_lee_roland_2008, title={Structural determination of large molecules through the reassembly of optimized fragments}, volume={27}, ISSN={["1873-4243"]}, DOI={10.1016/j.jmgm.2008.06.004}, abstractNote={The accurate determination of the optimized structures of large molecules is, computationally quite expensive. As an alternate to the conventional approaches to structural optimization, we have explored the accuracy and speed-up obtained when variants of the fragmentation optimization and recombination method (FORM) are used. Specifically, the method was applied to eight prototypical molecules -n-decane, hexa-alanine, a long conjugate hydrocarbon molecule, a large polar conjugated molecule, large (5,5) armchair single-walled carbon nanotubes, a salen-aluminum complex and a multiply H-bonded system (two conformers of vancomycin aglycon with Di-N-acetyl-l-Lys-d-Ala-d-Ala - without optimizing the structure of the whole molecules. We find that FORM can predict the structure of these molecules with an acceptable accuracy, all at a computational cost that is 2-11 times less than conventional quantum mechanical methods at the Hartree-Fock (HF), density functional theory (DFT) and MP2 level of accuracy. FORM may therefore represent a viable approach for the fast structural predictions of large molecules.}, number={3}, journal={JOURNAL OF MOLECULAR GRAPHICS & MODELLING}, author={Lee, Jung-Goo and Lee, Yoon Sup and Roland, Christopher}, year={2008}, month={Oct}, pages={364–375} }
 @article{odbadrakh_luo_lee_sagui_roland_2007, title={Theoretical investigation of the interaction of glycine with diamond C(100) and C(111) (2x1) surfaces}, volume={111}, ISSN={["1932-7455"]}, DOI={10.1021/jp073042j}, abstractNote={With density functional theory-based simulations, we have investigated the binding of the amino acid glycine on two of the most prominent diamond surfaces, that is, C(100) and C(111) (2 × 1), with a focus on the associated energetics, charge transfer, electronic, and structural characteristics. With regards to the dimerized C(100) surface, interaction is mostly via the amino group of the glycine molecule (both with and without H-atom abstraction) or the hydroxyl group with the loss of an associated H-atom. Barriers for these and other reactions were estimated with quantum chemistry methods. In contrast, the C(111) (2 × 1) surface was found to be mostly inert with respect to interactions with the glycine molecule.}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Odbadrakh, Khorgolkhuu and Luo, Xuan and Lee, Jung-Goo and Sagui, Celeste and Roland, Christopher}, year={2007}, month={Aug}, pages={12760–12767} }
 @article{lee_asciutto_babin_sagui_darden_roland_2006, title={Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations}, volume={110}, ISSN={["1520-5207"]}, DOI={10.1021/jp055809i}, abstractNote={The deprotonation of solvated formic acid was investigated theoretically with ab initio simulations. With the Car-Parrinello method, deprotonation and reprotonation by means of a proton wire were observed. The microscopics of these reactions were analyzed, and reveal the key role played by nearby water molecules in catalyzing the reactions. A constrained molecular dynamics calculation was carried out to estimate the dissociation free energy. Deprotonation of formic acid was further investigated with the recently developed metadynamics method using the formic acid oxygen coordination numbers as the collective variables. The determined free-energy landscape gives barriers similar to that obtained with the constrained free-energy calculation.}, number={5}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Lee, JG and Asciutto, E and Babin, V and Sagui, C and Darden, T and Roland, C}, year={2006}, month={Feb}, pages={2325–2331} }
 @article{lee_sagui_roland_2005, title={Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues}, volume={109}, ISSN={["1520-5207"]}, DOI={10.1021/jp0548117}, abstractNote={The recent rise of vancomycin-resistant enterococci (VRE) and vancomycin-resistant Staphylococcus aureus (VRSA) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin, avoparcin, teicoplanin, and ristocetin aglycons with dipetides, Ac-d-Ala-X, where X = d-Lac and d-Ser (characteristic of VREs) and X = d-Ala, Gly (characteristic of non-VREs), and a model "methylated d-Ala" CH(2)CH(CH(3))COO(-), in liquid as well as gas phase. The gas-phase ordering of the binding, from strongest to weakest, is Gly, d-Ala, d-Ser, CH(2)CH(CH(3))COO(-), and d-Lac. Calculations show that the order of the Gly and d-Ala binding is reversed in solution. The results are in good agreement with recent experimental findings.}, number={43}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Lee, JG and Sagui, C and Roland, C}, year={2005}, month={Nov}, pages={20588–20596} }
 @article{kim_kim_lee_2004, title={Black brane world from gravitating half sigma-lump}, number={1}, journal={Journal of High Energy Physics}, author={Kim, D. and Kim, Y. and Lee, J.}, year={2004} }
 @article{lee_sagui_roland_2004, title={First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini}, volume={126}, ISSN={["0002-7863"]}, DOI={10.1021/ja048645c}, abstractNote={The recent rise of vancomycin-resistant enterococci (VRE) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin and teicoplanin with d-Ala-d-Lac (characteristic of VREs) and d-Ala-d-Ala (characteristic of non-VREs). Binding of both antibiotics to d-Ala-d-Ala was found to be stronger by about 3-5 kcal/mol and due primarily to the oxygen-oxygen lone-pair repulsion characteristic of the antibiotic/d-Ala-d-Lac complex. These results are in good agreement with recent experimental findings.}, number={27}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Lee, JG and Sagui, C and Roland, C}, year={2004}, month={Jul}, pages={8384–8385} }
 @article{lee_jeong_lee_2003, title={An efficient method to compute partial atomic charges of large molecules using reassociation of fragments}, volume={24}, number={3}, journal={Bulletin of the Korean Chemical Society}, author={Lee, J. G. and Jeong, H. Y. and Lee, H.}, year={2003}, pages={369–376} }