@article{sarma_catella_san pedro_xiao_durmusoglu_menegatti_crook_magness_hall_2023, title={Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells}, volume={6}, ISSN={["2399-3642"]}, url={https://doi.org/10.1038/s42003-023-05242-x}, DOI={10.1038/s42003-023-05242-x}, abstractNote={Abstract Infections by Clostridioides difficile , a bacterium that targets the large intestine (colon), impact a large number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can be delivered to the gut and inhibit the biocatalytic activity of these toxins represent a promising therapeutic strategy to prevent and treat C. diff . infection. We describe an approach that combines a Pep tide B inding D esign (PepBD) algorithm, molecular-level simulations, a rapid screening assay to evaluate peptide:toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells. One peptide, SA1, is found to block TcdA toxicity in primary-derived human colon (large intestinal) epithelial cells. SA1 binds TcdA with a K D of 56.1 ± 29.8 nM as measured by surface plasmon resonance (SPR).}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Sarma, Sudeep and Catella, Carly M. and San Pedro, Ellyce T. and Xiao, Xingqing and Durmusoglu, Deniz and Menegatti, Stefano and Crook, Nathan and Magness, Scott T. and Hall, Carol K.}, year={2023}, month={Aug} } @article{xiao_kilgore_sarma_chu_menegatti_hall_2022, title={
De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G
}, volume={1669}, ISSN={["1873-3778"]}, DOI={10.1016/j.chroma.2022.462941}, abstractNote={Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet have a standard platform purification process for large-scale production. Short peptide ligands are viable alternatives to protein ligands in affinity chromatography. In this work, an integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments. The first cohort of designed sequences was tested experimentally using human polyclonal Fab, and the top performing sequence was selected as a prototype for a subsequent round of ligand refinement in silico. The resulting peptides were conjugated to chromatographic resins and evaluated via equilibrium and dynamic binding studies using human Fab-κ and Fab-λ. The equilibrium studies returned values of binding capacities up to 32 mg of Fab per mL of resin with mild affinity (KD ∼ 10-5 M) that are conducive to high product capture and recovery. Dynamic studies returned values of product yield up to ∼90%. Preliminary purification studies provided purities of 83-93% and yields of 11-89%. These results lay the groundwork for future development of these ligands towards biomanufacturing translation.}, journal={JOURNAL OF CHROMATOGRAPHY A}, author={Xiao, Xingqing and Kilgore, Ryan and Sarma, Sudeep and Chu, Wenning and Menegatti, Stefano and Hall, Carol K.}, year={2022}, month={Apr} } @article{sarma_herrera_xiao_hudalla_hall_2022, title={Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors}, volume={126}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.2c039188129J}, number={41}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Sarma, Sudeep and Herrera, Stephanie M. and Xiao, Xingqing and Hudalla, Gregory A. and Hall, Carol K.}, year={2022}, month={Oct}, pages={8129–8139} } @article{xiao_robang_sarma_le_helmicki_lambert_guerrero-ferreira_arboleda-echavarria_paravastu_hall_2022, title={Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides}, volume={1}, ISSN={["2752-6542"]}, DOI={10.1093/pnasnexus/pgac263}, abstractNote={Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyloid-forming peptides. Discontinuous molecular dynamics (DMD) simulation with the PRIME20 force field combined with the FoldAmyloid tool is used to examine the fibrilization kinetics of PepAD-generated peptides. PepAD screening of ∼10,000 7-mer peptides resulted in twelve top-scoring peptides with two distinct hydration properties. Our studies revealed that eight of the twelve in silico discovered peptides spontaneously form amyloid fibrils in the DMD simulations and that all eight have at least five residues that the FoldAmyloid tool classifies as being aggregation-prone. Based on these observations, we re-examined the PepAD-generated peptides in the sequence pool returned by PepAD and extracted five sequence patterns as well as associated sequence signatures for the 7-mer amyloid-forming peptides. Experimental results from Fourier transform infrared spectroscopy (FTIR), thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. This is the first attempt to use a computational approach to search for amyloid-forming peptides based on customized settings. Our efforts facilitate the identification of β-sheet-based self-assembling peptides, and contribute insights towards answering a fundamental scientific question: "What does it take, sequence-wise, for a peptide to self-assemble?".}, number={5}, journal={PNAS NEXUS}, author={Xiao, Xingqing and Robang, Alicia S. and Sarma, Sudeep and Le, Justin V. and Helmicki, Michael E. and Lambert, Matthew J. and Guerrero-Ferreira, Ricardo and Arboleda-Echavarria, Johana and Paravastu, Anant K. and Hall, Carol K.}, year={2022}, month={Nov} } @article{xiao_wang_seroski_wong_liu_paravastu_hudalla_hall_2021, title={De novo design of peptides that coassemble into beta sheet-based nanofibrils}, volume={7}, ISSN={["2375-2548"]}, DOI={10.1126/sciadv.abf7668}, abstractNote={Peptides’ hierarchical coassembly into nanostructures enables controllable fabrication of multicomponent biomaterials. In this work, we describe a computational and experimental approach to design pairs of charge-complementary peptides that selectively coassemble into β-sheet nanofibers when mixed together but remain unassembled when isolated separately. The key advance is a peptide coassembly design (PepCAD) algorithm that searches for pairs of coassembling peptides. Six peptide pairs are identified from a pool of ~106 candidates via the PepCAD algorithm and then subjected to DMD/PRIME20 simulations to examine their co-/self-association kinetics. The five pairs that spontaneously aggregate in kinetic simulations selectively coassemble in biophysical experiments, with four forming β-sheet nanofibers and one forming a stable nonfibrillar aggregate. Solid-state NMR, which is applied to characterize the coassembling pairs, suggests that the in silico peptides exhibit a higher degree of structural order than the previously reported CATCH(+/−) peptides.}, number={36}, journal={SCIENCE ADVANCES}, author={Xiao, Xingqing and Wang, Yiming and Seroski, Dillon T. and Wong, Kong M. and Liu, Renjie and Paravastu, Anant K. and Hudalla, Gregory A. and Hall, Carol K.}, year={2021}, month={Sep} } @article{wong_robang_lint_wang_dong_xiao_seroski_liu_shao_hudalla_et al._2021, title={Engineering beta-Sheet Peptide Coassemblies for Biomaterial Applications}, volume={12}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.1c04873}, abstractNote={Peptide coassembly, wherein at least two different peptides interact to form multicomponent nanostructures, is an attractive approach for generating functional biomaterials. Current efforts seek to design pairs of peptides, A and B, that form nanostructures (e.g., β-sheets with ABABA-type β-strand patterning) while resisting self-assembly (e.g., AAAAA-type or BBBBB-type β-sheets). To confer coassembly behavior, most existing designs have been based on highly charged variants of known self-assembling peptides; like-charge repulsion limits self-assembly while opposite-charge attraction promotes coassembly. Recent analyses using solid-state NMR and coarse-grained simulations reveal that preconceived notions of structure and molecular organization are not always correct. This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly.}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Wong, Kong M. and Robang, Alicia S. and Lint, Annabelle H. and Wang, Yiming and Dong, Xin and Xiao, Xingqing and Seroski, Dillon T. and Liu, Renjie and Shao, Qing and Hudalla, Gregory A. and et al.}, year={2021}, month={Dec} } @article{xiao_sarma_menegatti_crook_magness_hall_2021, title={In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A}, volume={17}, ISSN={["1554-8937"]}, url={https://doi.org/10.1021/acschembio.1c00743}, DOI={10.1021/acschembio.1c00743}, abstractNote={Clostridium difficile infection is mediated by two major exotoxins: toxins A (TcdA) and B (TcdB). Inhibiting the biocatalytic activities of these toxins with targeted peptide-based drugs can reduce the risk of C. difficile infection. In this work, we used a computational strategy that integrates a peptide binding design (PepBD) algorithm and explicit-solvent atomistic molecular dynamics simulation to determine promising toxin A-targeting peptides that can recognize and bind to the catalytic site of the TcdA glucosyltransferase domain (GTD). Our simulation results revealed that two out of three in silico discovered peptides, viz. the neutralizing peptides A (NPA) and B (NPB), exhibit lower binding free energies when bound to the TcdA GTD than the phage-display discovered peptide, viz. the reference peptide (RP). These peptides may serve as potential inhibitors against C. difficile infection. The efficacy of the peptides RP, NPA, and NPB to neutralize the cytopathic effects of TcdA was tested in vitro in human jejunum cells. Both phage-display peptide RP and in silico peptide NPA were found to exhibit strong toxin-neutralizing properties, thereby preventing the TcdA toxicity. However, the in silico peptide NPB demonstrates a relatively low efficacy against TcdA.}, number={1}, journal={ACS CHEMICAL BIOLOGY}, publisher={American Chemical Society (ACS)}, author={Xiao, Xingqing and Sarma, Sudeep and Menegatti, Stefano and Crook, Nathan and Magness, Scott T. and Hall, Carol K.}, year={2021}, month={Dec} } @article{xiao_kuang_burke_chushak_farmer_mirau_naik_hall_2020, title={In Silico Discovery and Validation of Neuropeptide-Y-Binding Peptides for Sensors}, volume={124}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.9b09439}, abstractNote={Wearable sensors for human health, performance, and state monitoring, which have a linear response to the binding of biomarkers found in sweat, saliva, or urine, are of current interest for many applications. A critical part of any device is a biological recognition element (BRE) that is able to bind a biomarker at the surface of a sensor with a high affinity and selectivity to produce a measurable signal response. In this study, we discover and compare 12-mer peptides that bind to neuropeptide Y (NPY), a stress and human health biomarker, using independent and complimentary experimental and computational approaches. The affinities of the NPY-binding peptides discovered by both methods are equivalent and below the micromolar level, which makes them suitable for application in sensors. The in silico design protocol for peptide-based BREs is low cost, highly efficient, and simple, suggesting its utility for discovering peptide binders to a variety of biomarker targets.}, number={1}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Xiao, Xingqing and Kuang, Zhifeng and Burke, B. J. and Chushak, Yaroslav and Farmer, Barry L. and Mirau, Peter A. and Naik, Rajesh R. and Hall, Carol K.}, year={2020}, month={Jan}, pages={61–68} } @article{reese_xiao_shanahan_driessche_fourches_carbonell_hall_menegatti_2020, title={Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities}, volume={1625}, ISSN={["1873-3778"]}, DOI={10.1016/j.chroma.2020.461237}, abstractNote={The quest for ligands alternative to Protein A for the purification of monoclonal antibodies (mAbs) has been pursued for almost three decades. Yet, the IgG-binding peptides known to date still fall short of the host cell protein (HCP) logarithmic removal value (LRV) set by Protein A media (2.5-3.1). In this study, we present an integrated computational-experimental approach leading to the discovery of peptide ligands that provide HCP LRVs on par with Protein A. First, the screening of 60,000 peptide variants was performed using a high-throughput search algorithm to identify sequences that ensure IgG affinity binding. Select sequences WQRHGI, MWRGWQ, RHLGWF, and GWLHQR were then negatively screened in silico against a panel of model HCPs to ensure the selection of peptides with high binding selectivity. Candidate ligands WQRHGI and MWRGWQ were conjugated to chromatographic resins and characterized by isothermal binding and breakthrough assays to quantify static and dynamic binding capacity (Qmax and DBC10%), respectively. The resulting Qmax were 52.6 mg of IgG per mL of adsorbent for WQRHGI and 57.48 mg/mL for MWRGWQ, while the DBC10% (2 minutes residence time) were 30.1 mg/mL for WQRHGI and 36.4 mg/mL for MWRGWQ. Evaluation of the peptides by isothermal titration calorimetry (ITC) confirmed the binding energy predicted in silico, and an amino acid scanning study corroborated the affinity-like binding activity of the peptides. WQRHGI-WorkBeads resin was finally characterized by purification of a monoclonal antibody from a Chinese Hamster Ovary (CHO) cell culture harvest, affording a remarkable HCP LRV of 2.7, and consistent product yield and purity over 100 chromatographic cycles. These results demonstrate the potential of WQRHGI as an effective alternative to Protein A for antibody purification.}, journal={JOURNAL OF CHROMATOGRAPHY A}, author={Reese, Hannah R. and Xiao, Xingqing and Shanahan, Calvin C. and Driessche, George A. and Fourches, Denis and Carbonell, Ruben G. and Hall, Carol K. and Menegatti, Stefano}, year={2020}, month={Aug} } @article{yan_tang_zhou_yang_xiao_chen_qin_sun_2019, title={All-silica zeolites screening for capture of toxic gases from molecular simulation}, volume={27}, ISSN={["2210-321X"]}, DOI={10.1016/j.cjche.2018.02.025}, abstractNote={The exhaust gases, including SO2, NH3, H2S, NO2, NO, and CO, are principal air pollutants due to their severe harms to the ecological environment. Zeolites have been considered as good absorbent candidates to capture the six exhaust gases. In this work, we performed grand canonical ensemble Monte Carlo (GCMC) simulations to examine the capability of 95 kinds of all-silica zeolites in the removal of the six toxic gases, and to predict the adsorption isotherms of the six gases on all the zeolites. The simulation results showed that, H2S, NO, NO2, CO and NH3 are well-captured by zeolite structures with accessible surface area of 1600–1800 m2·g− 1 and pore diameter of 0.6–0.7 nm, such as AFY and PAU, while SO2 is well-adsorbed by zeolites containing larger accessible surface area (1700–2700 m2·g− 1) and pore diameter (0.7–1.4 nm) at room temperature and an atmospheric pressure. However, at saturated adsorption, zeolites RWY, IRR, JSR, TSC, and ITT are found to exhibit better abilities to capture these gases. Our study provides useful computational insights in choosing and designing zeolite structures with high performance to remove toxic gases for air purification, thereby facilitating the development and application of exhaust gas-processing technology in green industry.}, number={1}, journal={CHINESE JOURNAL OF CHEMICAL ENGINEERING}, author={Yan, Zhiguo and Tang, Sai and Zhou, Xumiao and Yang, Li and Xiao, Xingqing and Chen, Houyang and Qin, Yuanhang and Sun, Wei}, year={2019}, month={Jan}, pages={174–181} } @article{xiejun_xingqing_shouhong_hongai_2019, title={Computational Study of Thermosensitivity of Liposomes Modulated by Leucine Zipper-Structured Lipopeptides}, volume={35}, ISSN={["1000-6818"]}, DOI={10.3866/PKU.WHXB201806034}, number={6}, journal={ACTA PHYSICO-CHIMICA SINICA}, author={Xiejun, Xu and Xingqing, Xiao and Shouhong, Xu and Hongai, Liu}, year={2019}, pages={598–606} } @article{li_chen_xiao_yang_peng_qin_wang_sun_wang_2019, title={Computational study of transition states for reaction path of energetic material TKX-50}, volume={37}, ISSN={["1545-8822"]}, DOI={10.1080/07370652.2019.1590482}, abstractNote={Dihydroxylammonium5,5′-bistetrazole-1,1′-diolate (TKX-50) is considered as one of the new ionic energetic materials. In this study, we employed density functional theory (DFT) method to calculate the reaction path of TKX-50 and search its optimized configurations of reactants, reactant complexes (RCs), transition states (TSs), product complexes (PCs), and products. We proposed 10 simple reactions in the reaction path, and determined their transition states. Among these TSs, six of them have lower energies than those of reactants. The equilibrium constants, which indicate the limitation of reactions, were computed from the difference of Gibbs free energy with temperature change. Based on the proposed reaction path, the reaction mechanism of TKX-50 was provided.}, number={2}, journal={JOURNAL OF ENERGETIC MATERIALS}, author={Li, Miao and Chen, Houyang and Xiao, Xingqing and Yang, Li and Peng, Changjun and Qin, Yuanhang and Wang, Tielin and Sun, Wei and Wang, Cunwen}, year={2019}, month={Apr}, pages={240–250} } @article{tong_xiao_liang_solms_huo_he_zhang_2019, title={Insights into the solvation and dynamic behaviors of a lithium salt in organic- and ionic liquid-based electrolytes}, volume={21}, ISSN={["1463-9084"]}, DOI={10.1039/c9cp01848d}, abstractNote={New-generation lithium-ion batteries use ionic liquids (ILs) as electrolyte solutions, greatly enhancing the safety and energy storage capacity of the battery. Fundamental molecular insights are useful for understanding the advantages of high conductivity of IL solvent electrolytes over organic solvent ones. In this work, we computationally studied two organic solvents (DMC and DEC) and four IL solvents ([Cnmim][BF4] and [Cnmim][TFSI] (n = 2, 4)) to examine the physicochemical properties of high concentration electrolytes. As expected, the IL solvent electrolytes exhibit higher density and viscosity, and larger self-diffusion coefficients and conductivity than the organic solvent electrolytes. Further, the microstructures of the lithium salt LiTFSI in various solvent electrolytes were investigated to explore the effect of the organic and IL solvents on the ionic association of the ions Li+ and TFSI-. The structural analysis of LiTFSI revealed that the organic solvents restrict the free motion of the ions, reducing the conductivity of the electrolytes. The [BF4]-type IL electrolytes have higher conductivity than the [TFSI]-type IL electrolytes, especially [C4mim][BF4] with the highest conductivity among the IL-based electrolytes. More importantly, it was proved that the dissolution of LiTFSI in the IL solvents is an anion-driven process.}, number={35}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Tong, Jiahuan and Xiao, Xingqing and Liang, Xiaodong and Solms, Nicolas and Huo, Feng and He, Hongyan and Zhang, Suojiang}, year={2019}, month={Sep}, pages={19216–19225} } @article{xiao_kuang_slocik_tadepalli_brothers_kim_mirau_butkus_farmer_singamaneni_et al._2018, title={Advancing Peptide-Based Biorecognition Elements for Biosensors Using in-Silico Evolution}, volume={3}, ISSN={["2379-3694"]}, DOI={10.1021/acssensors.8b00159}, abstractNote={Sensors for human health and performance monitoring require biological recognition elements (BREs) at device interfaces for the detection of key molecular biomarkers that are measurable biological state indicators. BREs, including peptides, antibodies, and nucleic acids, bind to biomarkers in the vicinity of the sensor surface to create a signal proportional to the biomarker concentration. The discovery of BREs with the required sensitivity and selectivity to bind biomarkers at low concentrations remains a fundamental challenge. In this study, we describe an in-silico approach to evolve higher sensitivity peptide-based BREs for the detection of cardiac event marker protein troponin I (cTnI) from a previously identified BRE as the parental affinity peptide. The P2 affinity peptide, evolved using our in-silico method, was found to have ∼16-fold higher affinity compared to the parent BRE and ∼10 fM (0.23 pg/mL) limit of detection. The approach described here can be applied towards designing BREs for other biomarkers for human health monitoring.}, number={5}, journal={ACS SENSORS}, author={Xiao, Xingqing and Kuang, Zhifeng and Slocik, Joseph M. and Tadepalli, Sirimuvva and Brothers, Michael and Kim, Steve and Mirau, Peter A. and Butkus, Claire and Farmer, Barry L. and Singamaneni, Srikanth and et al.}, year={2018}, month={May}, pages={1024–1031} } @article{zhou_su_chen_xiao_qin_yang_yan_sun_2018, title={Capture of pure toxic gases through porous materials from molecular simulations}, volume={116}, ISSN={["1362-3028"]}, DOI={10.1080/00268976.2018.1440019}, abstractNote={In the last three decades, the air pollution is the main problem to affect human health and the environment in China and its contaminants include SO2, NH3, H2S, NO2, NO and CO. In this work, we employed grand canonical Monte Carlo simulations to investigate the adsorption capability of metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) for these toxic gases. Eighty-nine MOFs and COFs were studied, and top-10 adsorption materials were screened for each toxic gas at room temperature. Dependence of the adsorption performance on the geometry and constructed element of MOFs/COFs was determined and the adsorption conditions were optimised. The open metal sites have mainly influenced the adsorption of NH3, H2S, NO2 and NO. Especially, the X-DOBDC and XMOF-74 (X = Mg, Co, Ni, Zn) series of materials containing open metal sites are all best performance for adsorption of NH3 to illustrate the importance of electrostatic interaction. Our simulation results also showed that ZnBDC and IRMOF-13 are good candidates to capture the toxic gases NH3, H2S, NO2, NO and CO. This work provides important insights in screening MOF and COF materials with satisfactory performance for toxic gas removal.}, number={15-16}, journal={MOLECULAR PHYSICS}, author={Zhou, Xumiao and Su, Zejun and Chen, Houyang and Xiao, Xingqing and Qin, Yuanhang and Yang, Li and Yan, Zhiguo and Sun, Wei}, year={2018}, pages={2095–2107} } @article{kang_xiao_huang_yuan_tang_dai_zeng_2018, title={Potent aromatase inhibitors and molecular mechanism of inhibitory action}, volume={143}, ISSN={["1768-3254"]}, DOI={10.1016/j.ejmech.2017.11.057}, abstractNote={Estrogen is a significant factor in the maintenance and progression of hormone-dependent breast cancer. As well known, aromatase mediates the production of estrogen. Thus, inhibition of aromatase with chemical molecules has been considered to be an effective treatment for estrogen receptor-positive (ER+) breast cancer. In this work, we designed and synthesized a series of novel non-steroidal molecules containing 2-phenylindole scaffold and moiety of either imidazole or 1,2,4-triazole to enhance their binding capacity with the aromatase. Among these molecules, a compound named as 8o was confirmed experimentally to have the highest inhibitory activity to aromatase. Further cell activity assay proved that compound 8o has low cytotoxicity and is a promising lead for developing novel aromatase inhibitors. Molecular modeling and simulation techniques were performed to identify the binding modes of letrozole and 8o with the aromatase. Analysis of energy of the two compound-aromatase complexes revealed that the 8o has low binding energy (strong binding affinity) to the aromatase as compared to letrozole, which was in accordance with the experimental results. As concluded, a combination of experimental and computational approaches facilitates us to understand the molecular mechanism of inhibitory action and discover more potent non-steroidal AIs against aromatase, thereby opening up a novel therapeutic strategy for hormone-dependent breast cancer.}, journal={EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY}, author={Kang, Hongjun and Xiao, Xingqing and Huang, Chao and Yuan, Yan and Tang, Dongyan and Dai, Xiaochang and Zeng, Xianghui}, year={2018}, month={Jan}, pages={426–437} } @article{xiao_wang_leonard_hall_2017, title={Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm}, volume={13}, ISSN={["1549-9626"]}, DOI={10.1021/acs.jctc.7b00714}, abstractNote={To enhance the sampling efficiency of our computational peptide-design algorithm in conformational space, the concerted rotation (CONROT) technique is extended to enable larger conformational perturbations of peptide chains. This allows us to make relatively large peptide conformation changes during the process of designing peptide sequences to bind with high affinity to a specific target. Searches conducted using the new algorithm identified six potential λ N(2-22) peptide variants, called B1-B6, which bind to boxB RNA with high affinity. The results of explicit-solvent atomistic molecular dynamics simulations revealed that four of the evolved peptides, viz. B1, B2, B3, and B5, are excellent candidate binders to the target boxB RNA as they have lower binding free energies than the original λ N(2-22) peptide. Three of the four peptides, B2, B3, and B5, result from searches that contain both sequence and conformation changes, indicating that adding backbone motif changes to the peptide-design algorithm improves its performance considerably.}, number={11}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, author={Xiao, Xingqing and Wang, Yiming and Leonard, Joshua N. and Hall, Carol K.}, year={2017}, month={Nov}, pages={5709–5720} } @article{xiao_hung_leonard_hall_2016, title={Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned N peptide binds boxB RNA}, volume={37}, ISSN={["1096-987X"]}, DOI={10.1002/jcc.24466}, abstractNote={Our previously developed peptide-design algorithm was improved by adding an energy minimization strategy which allows the amino acid sidechains to move in a broad configuration space during sequence evolution. In this work, the new algorithm was used to generate a library of 21-mer peptides which could substitute for λ N peptide in binding to boxB RNA. Six potential peptides were obtained from the algorithm, all of which exhibited good binding capability with boxB RNA. Atomistic molecular dynamics simulations were then conducted to examine the ability of the λ N peptide and three best evolved peptides, viz. Pept01, Pept26, and Pept28, to bind to boxB RNA. Simulation results demonstrated that our evolved peptides are better at binding to boxB RNA than the λ N peptide. Sequence searches using the old (without energy minimization strategy) and new (with energy minimization strategy) algorithms confirm that the new algorithm is more effective at finding good RNA-binding peptides than the old algorithm. © 2016 Wiley Periodicals, Inc.}, number={27}, journal={JOURNAL OF COMPUTATIONAL CHEMISTRY}, author={Xiao, Xingqing and Hung, Michelle E. and Leonard, Joshua N. and Hall, Carol K.}, year={2016}, month={Oct}, pages={2423–2435} } @article{xu_xiao_xu_liu_2016, title={Computational insights into the destabilization of alpha-helical conformations formed by leucine zipper peptides in response to temperature}, volume={18}, ISSN={["1463-9084"]}, DOI={10.1039/c6cp05145f}, abstractNote={The computed transition temperature of leucine zipper peptides is 319.1 K, which is in quantitative agreement with the experimental measurement, 321.1 K.}, number={36}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Xu, Xiejun and Xiao, Xingqing and Xu, Shouhong and Liu, Honglai}, year={2016}, month={Sep}, pages={25465–25473} } @article{xiao_agris_hall_2016, title={Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success}, volume={84}, ISSN={["1097-0134"]}, DOI={10.1002/prot.25021}, abstractNote={A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search.}, number={5}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Xiao, Xingqing and Agris, Paul F. and Hall, Carol K.}, year={2016}, month={May}, pages={700–711} } @article{xiao_zhao_yang_liang_ren_2016, title={Probe the Binding Mode of Aristololactam-beta-D-glucoside to Phenylalanine Transfer RNA in Silico}, volume={1}, ISSN={["2365-6549"]}, DOI={10.1002/slct.201600603}, abstractNote={Abstract Understanding the interactions of drug molecules with biomacromolecules at a micro‐scale level is essential to design potent drugs for the treatments of human genome diseases. To unravel the mechanism of binding of aristololactam‐β‐D‐glucoside (ADG) and phenylalanine transfer RNA (tRNA Phe ), an integrated computational strategy combining quantum mechanics (QM) calculation, molecular docking and atomistic molecular dynamics (MD) simulation was present in this work. QM calculations were performed to derive the partial charges of ADG, molecular docking was used to determine the binding poses of ADG on the tRNA Phe , and atomistic MD simulations were conducted to examine the thermal stability of five predicted binding poses for the complex of ADG and the tRNA Phe . The binding free energies of the five complexes were then calculated using the molecular mechanics/generalized born surface area approach with the variable internal dielectric constant model. By comparing computed affinities and experimentally‐measured values in the binding free energy, we identified a most likely binding structure of ADG and the tRNA Phe . Further analysis of energy of the ADG‐tRNA complex revealed that the aristololactam of ADG provides binding specificity to the tRNA Phe , and the D‐glucoce contributes to the affinity for binding with the tRNA Phe .}, number={17}, journal={CHEMISTRYSELECT}, author={Xiao, Xingqing and Zhao, Binwu and Yang, Li and Liang, Xiaodong and Ren, Yingqian}, year={2016}, month={Oct}, pages={5430–5439} } @article{xiao_zhao_agris_hall_2016, title={Simulation study of the ability of a computationally-designed peptide to recognize target tRNA(Lys3) and other decoy tRNAs}, volume={25}, ISSN={["1469-896X"]}, DOI={10.1002/pro.3056}, abstractNote={Abstract In this paper, we investigate the ability of our computationally‐designed peptide, Pept10 (PNWNGNRWLNNCLRG), to recognize the anticodon stem and loop (ASL) domain of the hypermodified tRNA Lys3 (mcm 5 s 2 U 34 ,ms 2 t 6 A 37 ), a reverse transcription primer of HIV replication. Five other ASLs, the singly modified ASL Lys3 (ms 2 t 6 A 37 ), ASL Lys3 (s 2 U 34 ), ASL Lys3 (Ψ 39 ), ASL Lys1,2 (t 6 A 37 ), and ASL Glu (s 2 U 34 ), were used as decoys. Explicit‐solvent atomistic molecular dynamics simulations were performed to examine the process of binding of Pept10 with the target ASL Lys3 (mcm 5 s 2 U 34 ,ms 2 t 6 A 37 ) and the decoy ASLs. Simulation results demonstrated that Pept10 is capable of recognizing the target ASL Lys3 (mcm 5 s 2 U 34 ,ms 2 t 6 A 37 ) as well as one of the decoys, ASL Lys3 (Ψ 39 ), but screens out the other four decoy ASLs. The interchain van der Waals (VDW) and charge–charge (ELE + EGB) energies for the two best complexes were evaluated to shed light on the molecular recognition mechanism between Pept10 and ASLs. The results indicated that Pept10 recognizes and binds to the target ASL Lys3 (mcm 5 s 2 U 34 ,ms 2 t 6 A 37 ) through residues W 3 and R 7 which interact with the nucleotides mcm 5 s 2 U 34 , U 35 , and ms 2 t 6 A 37 via the interchain VDW energy. Pept10 also recognizes the decoy ASL Lys3 (Ψ 39 ) through residue R 14 which contacts the nucleotide U 36 via the interchain VDW energy. Regardless of the type of ASL, the positively charged arginines on Pept10 are attracted to the negatively charged phosphate linkages on the ASL via the interchain ELE + EGB energy, thereby enhancing the binding affinity.}, number={12}, journal={PROTEIN SCIENCE}, author={Xiao, Xingqing and Zhao, Binwu and Agris, Paul F. and Hall, Carol K.}, year={2016}, month={Dec}, pages={2243–2255} } @article{xiao_agris_hall_2015, title={Designing Peptide Sequences in Flexible Chain Conformations to Bind RNA: A Search Algorithm Combining Monte Carlo, Self-Consistent Mean Field and Concerted Rotation Techniques}, volume={11}, ISSN={["1549-9626"]}, DOI={10.1021/ct5008247}, abstractNote={A search algorithm combining Monte Carlo, self-consistent mean field, and concerted rotation techniques was developed to discover peptide sequences that are reasonable HIV drug candidates due to their exceptional binding to human tRNAUUULys3, the primer of HIV replication. The search algorithm allows for iteration between sequence mutations and conformation changes during sequence evolution. Searches conducted for different classes of peptides identified several potential peptide candidates. Analysis of the energy revealed that the asparagine and cysteine at residues 11 and 12 play important roles in “recognizing” tRNALys3 via van der Waals interactions, contributing to binding specificity. Arginines preferentially attract the phosphate linkage via charge–charge interaction, contributing to binding affinity. Evaluation of the RNA/peptide complex’s structure revealed that adding conformation changes to the search algorithm yields peptides with better binding affinity and specificity to tRNALys3 than a previous mutation-only algorithm.}, number={2}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, author={Xiao, Xingqing and Agris, Paul F. and Hall, Carol K.}, year={2015}, month={Feb}, pages={740–752} } @article{xiao_zhao_ren_2015, title={Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 1. Layer thickness of a curved monolayer}, volume={633}, ISSN={["1873-4448"]}, DOI={10.1016/j.cplett.2015.05.016}, abstractNote={Strong segregation limited theory was employed to deduce the expression for free energy of a curved (A–B) monolayer that is a basic repeating unit in multi-layered concentric structure. The free energy of the monolayer in different curved conditions can be evaluated. Using such cylindrical confinement model, we examined the influences of asymmetry of diblock copolymers on the layer thickness of a curved monolayer. For the diblock copolymers of f = 0.4, the optimal thickness has a slight increase and then decrease as the curvature increases; while for f = 0.6, the optimal thickness has a continuous decrease as the curvature increases.}, journal={CHEMICAL PHYSICS LETTERS}, author={Xiao, Xingqing and Zhao, Binwu and Ren, Yingqian}, year={2015}, month={Jul}, pages={58–64} } @article{xiao_zhao_yang_ren_2015, title={Effect of curvature on properties of diblock copolymers confined between two coaxial cylinders: 2. Domain adjustment in a curved bilayer}, volume={639}, ISSN={["1873-4448"]}, DOI={10.1016/j.cplett.2015.10.032}, abstractNote={We study the phase behavior of diblock copolymers in a curved bilayer. Three aspects are discussed in detail: domain size distributions of the two adjacent monolayers within the film, optimal film thickness for a bilayer, and structural transition from a monolayer to a bilayer. One major finding is the determination of transition point in film thickness where the layer-type structure goes from monolayer to bilayer. At high confinement, the transition point increases as the curvature increases regardless of the symmetry of diblock copolymers. At low confinement, the transition point might increase or decrease, depending on the symmetry of diblock copolymers.}, journal={CHEMICAL PHYSICS LETTERS}, author={Xiao, Xingqing and Zhao, Binwu and Yang, Li and Ren, Yingqian}, year={2015}, month={Oct}, pages={326–334} } @article{xiao_agris_hall_2015, title={Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico}, volume={33}, ISSN={["1538-0254"]}, DOI={10.1080/07391102.2013.869660}, abstractNote={The mechanism by which proteins recognize and bind the post-transcriptional modifications of RNAs is unknown, yet these interactions play important functions in biology. Atomistic molecular dynamics simulations were performed to examine the folding of the model peptide chain –RVTHHAFLGAHRTVG– and the complex formed by the folded peptide with the native anticodon stem and loop of the human tRNALys3 (hASLLys3) in order to explore the binding mechanism. By analyzing and comparing two folded conformations of this peptide obtained from the folding simulation, we found that the van der Waals (VDW) energy is necessary for the thermal stability of the peptide, and the charge–charge (ELE + EGB) energy is crucial for determining the three-dimensional folded structure of the peptide backbone. Subsequently, two conformations of the peptide were employed to investigate their binding behaviors to hASLLys3. The metastable folded peptide was found to bind to hASLLys3 much easier than the stable folded peptide in the binding simulations. An energetic analysis reveals that the VDW energy favors the binding, whereas the ELE + EGB energies disfavor the binding. Arginines on the peptide preferentially attract the phosphate backbone via the inter-chain ELE + EGB interaction, significantly contributing to the binding affinity. The hydrophobic phenylalanine interacts with the anticodon loop of hASLLys3 via the inter-chain VDW interaction, significantly contributing to the binding specificity.}, number={1}, journal={JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS}, author={Xiao, Xingqing and Agris, Paul F. and Hall, Carol K.}, year={2015}, month={Jan}, pages={14–27} } @article{curtis_xiao_sofou_hall_2015, title={Phase Separation Behavior of Mixed Lipid Systems at Neutral and Low pH: Coarse-Grained Simulations with DMD/LIME}, volume={31}, ISSN={["0743-7463"]}, DOI={10.1021/la504082x}, abstractNote={We extend LIME, an intermediate resolution, implicit solvent model for phospholipids previously used in discontinuous molecular dynamics simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer formation at 325 K, to the description of the geometry and energetics of 1,2-distearoyl-sn-glycero-3-phospho-l-serine (DSPS) and 1,2-dihenarachidoyl-sn-glycero-3-phosphocholine (21PC) and mixtures thereof at both neutral and low pH at 310 K. A multiscale modeling approach is used to calculate the LIME parameters from atomistic simulation data on a mixed DPPC/DSPS system at different pH values. In the model, 17 coarse-grained sites represent DSPS and 18 coarse-grained sites represent 21PC. Each of these coarse-grained sites is classified as 1 of 9 types. LIME/DMD simulations of equimolar bilayers show the following: (1) 21PC/DSPS bilayers with and without surface area restrictions separate faster at low pH than at neutral pH, (2) 21PC/DSPS systems separate at approximately the same rate regardless of whether they are subjected to surface area restrictions, and (3) bilayers with a molar ratio of 9:1 (21PC:DSPS) phase separate to form heterogeneous domains faster at low pH than at neutral pH. Our results are consistent with experimental findings of Sofou and co-workers (Bandekar et al. Mol. Pharmaceutics, 2013, 10, 152–160; Karve et al. Biomaterials, 2010, 31, 4409–4416) that more doxorubicin is released from 21PC/DSPS liposomes at low pH than at neutral pH, presumably because greater phase separation is achieved at low pH than at neutral pH. These are the first molecular-level simulations of the phase separation in mixed lipid bilayers induced by a change in pH.}, number={3}, journal={LANGMUIR}, author={Curtis, Emily M. and Xiao, Xingqing and Sofou, Stavroula and Hall, Carol K.}, year={2015}, month={Jan}, pages={1086–1094} } @article{spears_xiao_hall_agris_2014, title={Amino Acid Signature Enables Proteins to Recognize Modified tRNA}, volume={53}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi401174h}, DOI={10.1021/bi401174h}, abstractNote={Human tRNA(Lys3)UUU is the primer for HIV replication. The HIV-1 nucleocapsid protein, NCp7, facilitates htRNA(Lys3)UUU recruitment from the host cell by binding to and remodeling the tRNA structure. Human tRNA(Lys3)UUU is post-transcriptionally modified, but until recently, the importance of those modifications in tRNA recognition by NCp7 was unknown. Modifications such as the 5-methoxycarbonylmethyl-2-thiouridine at anticodon wobble position-34 and 2-methylthio-N(6)-threonylcarbamoyladenosine, adjacent to the anticodon at position-37, are important to the recognition of htRNA(Lys3)UUU by NCp7. Several short peptides selected from phage display libraries were found to also preferentially recognize these modifications. Evolutionary algorithms (Monte Carlo and self-consistent mean field) and assisted model building with energy refinement were used to optimize the peptide sequence in silico, while fluorescence assays were developed and conducted to verify the in silico results and elucidate a 15-amino acid signature sequence (R-W-Q/N-H-X2-F-Pho-X-G/A-W-R-X2-G, where X can be most amino acids, and Pho is hydrophobic) that recognized the tRNA's fully modified anticodon stem and loop domain, hASL(Lys3)UUU. Peptides of this sequence specifically recognized and bound modified htRNA(Lys3)UUU with an affinity 10-fold higher than that of the starting sequence. Thus, this approach provides an effective means of predicting sequences of RNA binding peptides that have better binding properties. Such peptides can be used in cell and molecular biology as well as biochemistry to explore RNA binding proteins and to inhibit those protein functions.}, number={7}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Spears, Jessica L. and Xiao, Xingqing and Hall, Carol K. and Agris, Paul F.}, year={2014}, month={Feb}, pages={1125–1133} } @article{xiao_hall_agris_2014, title={The design of a peptide sequence to inhibit HIV replication: a search algorithm combining Monte Carlo and self-consistent mean field techniques}, volume={32}, ISSN={["1538-0254"]}, DOI={10.1080/07391102.2013.825757}, abstractNote={We developed a search algorithm combining Monte Carlo (MC) and self-consistent mean field techniques to evolve a peptide sequence that has good binding capability to the anticodon stem and loop (ASL) of human lysine tRNA species, tRNALys3, with the ultimate purpose of breaking the replication cycle of human immunodeficiency virus-1. The starting point is the 15-amino-acid sequence, RVTHHAFLGAHRTVG, found experimentally by Agris and co-workers to bind selectively to hypermodified tRNALys3. The peptide backbone conformation is determined via atomistic simulation of the peptide-ASLLys3 complex and then held fixed throughout the search. The proportion of amino acids of various types (hydrophobic, polar, charged, etc.) is varied to mimic different peptide hydration properties. Three different sets of hydration properties were examined in the search algorithm to see how this affects evolution to the best-binding peptide sequences. Certain amino acids are commonly found at fixed sites for all three hydration states, some necessary for binding affinity and some necessary for binding specificity. Analysis of the binding structure and the various contributions to the binding energy shows that: 1) two hydrophilic residues (asparagine at site 11 and the cysteine at site 12) “recognize” the ASLLys3 due to the VDW energy, and thereby contribute to its binding specificity and 2) the positively charged arginines at sites 4 and 13 preferentially attract the negatively charged sugar rings and the phosphate linkages, and thereby contribute to the binding affinity.}, number={10}, journal={JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS}, author={Xiao, Xingqing and Hall, Carol K. and Agris, Paul F.}, year={2014}, pages={1523–1536} }