Engineering topics

Choudhuri, Indrani

Publications and source records attributed to Choudhuri, Indrani.

5 records

DOE OSTI2025

Using phage display for rational engineering of a higher-affinity humanized 3’ phosphohistidine-specific antibody

Abstract Histidine phosphorylation is a non-canonical post-translational modification (PTM), with 1-phosphohistidine (1-pHis) and 3-phosphohistidine (3-pHis) isoforms, that is understudied due to a lack of robust reagents, including high-affinity pHis-specific antibodies. Engineering pHis antibodies is challenging due to the labile nature of its phosphoramidate (P-N) bond. We developed a strategy for in vitro engineering of antibodies for the detection of native 3-pHis targets, in which the rabbit SC44-8 anti-3-pTza mAb is humanized into a scaffold (hSC44) that is suitable for phage display. Six unique Fab phage-displayed hSC44 scaffold libraries were screened for antibodies that bound 3-pHis with higher affinity and had specificity for 3-pHis versus 3-pTza. hSC44.20N32F L , the best engineered antibody, has ~10-fold higher affinity for 3-pHis than parental hSC44. Eleven new Fab structures, including the first antibody-pHis peptide structures, together with structural and quantum mechanical calculations, provided molecular insights into 3-pHis and 3-pTza discrimination by hSC44.20N32F L and the increased affinity obtained through engineering. We demonstrated the utility of these high-affinity 3-pHis-specific antibodies for the recognition of pHis proteins in mammalian cells by immunoblotting and immunofluorescence staining. Our work describes a general method for engineering labile PTM-specific antibodies and provides novel antibodies for investigating the role of 3-pHis in cell biology.

Martyn, Gregory D.↗

DOE OSTI2023

Computational quantum chemistry of metal–organic frameworks

Metal–organic frameworks (MOFs) have premium exceptional properties for a variety of functions, such as gas separation and storage and catalysis. The large variety of possible inorganometallic nodes and organic linkers provide an almost unlimited number of combinations for assembling MOFs, which makes the experimental characterization and examination of all potentially useful combinations practically impossible. Furthermore, experimental studies of MOFs typically fall short in uncovering crucial details regarding their mechanisms of action or the molecular details responsible for their functional properties, such as the nature of adsorbate binding or the structures of transition states. Computational modeling has, therefore, become an efficient and important tool for strategizing the functionalization of MOFs and explicating the mechanisms of their functions. Furthermore, we review the computational methodologies used for computational studies of MOFs, especially Kohn–Sham density functional theory and combined quantum mechanical and molecular mechanical methods for calculating their structural, electronic, and magnetic properties, as well as for understanding the mechanisms of MOFs' applications to magetic devices, thermal conduction, gas adsorption, separation, storage, and sensing, thermal catalysis, photocatalysis, and electrocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants

HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Calculating and Characterizing the Charge Distributions in Solids

Accurate estimation of the partial atomic charges on metal centers is useful for understanding electronic and catalytic properties of materials. However, different methods of calculating these charges may give quite different results; this issue has been more widely studied for molecules than for solids. Here we study the charges on the metal centers of a test set of 18 solids containing transition metals by using density functional theory with several density functionals (PBE, PBE+U, TPSS, revTPSS, HLE17, revM06-L, B3LYP, B3LYP*, and other exchange-modified B3LYP functionals) and four charge models (Bader, Hirshfeld, CM5, and DDEC6). The test set contains 12 systems with nonmagnetic metal centers (eight metal oxides (MO 2 ), two metal sulfides (MS 2 ), and two metal selenides (MSe 2 )) and six ferromagnetic transition metal complexes. Our study shows that, among the four types of charges, Bader charges are the highest and Hirshfeld charges are the lowest for all the systems, regardless of the functional being used. The CM5 charges are bigger than DDEC6 charges for MX 2 with M = Ti or Mo and X = S or Se, but for the other 14 cases they are lower. We found that the most of the systems are sensitive to the Hubbard U parameters in PBE+U and to the percentage X of Hartree–Fock exchange in exchange-modified B3LYP; as we increase U or X, the charges on the metal atoms in MX 2 increase steadily. Testing different density functionals shows charges calculated with higher Hubbard U parameters in PBE+U are comparable to B3LYP (with 20% Hartree–Fock exchange). Among four meta-GGA functionals studied, the charges with HLE17 have the closest agreement with B3LYP. In conclusion, the variation of charges with choice of charge model is greater than the variation with choice of density functional.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Photogenerated Charge Separation in a CdSe Nanocluster Encapsulated in a Metal–Organic Framework for Improved Photocatalysis

Nanoclusters encapsulated in a metal–organic framework (MOF) are the subject of intense interest because of their high promise for photocatalysis. We show computationally that a CdSe nanocluster incorporated into NU-1000 (Cd 6 Se 6 @NU-1000) allows electron transfer from a visible-light photo-excited organic linker to the lowest unoccupied crystal orbital of the inorganic cluster, which can lead to charge separation. Substituents on the linker can be used to tune the band position and the band gap of the whole composite (Cd 6 Se 6 @NU-1000), and this makes it possible to perform the water splitting reaction under visible light. Here, the achievement of charge separation within the MOF leads to longer life of the excited states, and as a result, it can enhance the photocatalytic activity of the system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗