Search Results - "Bera, Asim K"

Reconfigurable asymmetric protein assemblies through implicit negative design by Sahtoe, Danny D, Praetorius, Florian, Courbet, Alexis, Hsia, Yang, Wicky, Basile I M, Edman, Natasha I, Miller, Lauren M, Timmermans, Bart J R, Decarreau, Justin, Morris, Hana M, Kang, Alex, Bera, Asim K, Baker, David

“…Asymmetric multiprotein complexes that undergo subunit exchange play central roles in biology but present a challenge for design because the components must…”
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Directing polymorph specific calcium carbonate formation with de novo protein templates by Davila-Hernandez, Fatima A., Jin, Biao, Pyles, Harley, Zhang, Shuai, Wang, Zheming, Huddy, Timothy F., Bera, Asim K., Kang, Alex, Chen, Chun-Long, De Yoreo, James J., Baker, David

“…Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces…”
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Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites by Hosseinzadeh, Parisa, Watson, Paris R., Craven, Timothy W., Li, Xinting, Rettie, Stephen, Pardo-Avila, Fátima, Bera, Asim K., Mulligan, Vikram Khipple, Lu, Peilong, Ford, Alexander S., Weitzner, Brian D., Stewart, Lance J., Moyer, Adam P., Di Piazza, Maddalena, Whalen, Joshua G., Greisen, Per Jr, Christianson, David W., Baker, David

“…Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site…”
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Design of multi-scale protein complexes by hierarchical building block fusion by Hsia, Yang, Mout, Rubul, Sheffler, William, Edman, Natasha I., Vulovic, Ivan, Park, Young-Jun, Redler, Rachel L., Bick, Matthew J., Bera, Asim K., Courbet, Alexis, Kang, Alex, Brunette, T. J., Nattermann, Una, Tsai, Evelyn, Saleem, Ayesha, Chow, Cameron M., Ekiert, Damian, Bhabha, Gira, Veesler, David, Baker, David

“…A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing…”
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Large-scale design and refinement of stable proteins using sequence-only models by Singer, Jedediah M, Novotney, Scott, Strickland, Devin, Haddox, Hugh K, Leiby, Nicholas, Rocklin, Gabriel J, Chow, Cameron M, Roy, Anindya, Bera, Asim K, Motta, Francis C, Cao, Longxing, Strauch, Eva-Maria, Chidyausiku, Tamuka M, Ford, Alex, Ho, Ethan, Zaitzeff, Alexander, Mackenzie, Craig O, Eramian, Hamed, DiMaio, Frank, Grigoryan, Gevorg, Vaughn, Matthew, Stewart, Lance J, Baker, David, Klavins, Eric

“…Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare…”
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De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8 by Roy, Anindya, Shi, Lei, Chang, Ashley, Dong, Xianchi, Fernandez, Andres, Kraft, John C., Li, Jing, Le, Viet Q., Winegar, Rebecca Viazzo, Cherf, Gerald Maxwell, Slocum, Dean, Poulson, P. Daniel, Casper, Garrett E., Vallecillo-Zúniga, Mary L., Valdoz, Jonard Corpuz, Miranda, Marcos C., Bai, Hua, Kipnis, Yakov, Olshefsky, Audrey, Priya, Tanu, Carter, Lauren, Ravichandran, Rashmi, Chow, Cameron M., Johnson, Max R., Cheng, Suna, Smith, McKaela, Overed-Sayer, Catherine, Finch, Donna K., Lowe, David, Bera, Asim K., Matute-Bello, Gustavo, Birkland, Timothy P., DiMaio, Frank, Raghu, Ganesh, Cochran, Jennifer R., Stewart, Lance J., Campbell, Melody G., Van Ry, Pam M., Springer, Timothy, Baker, David

“…The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds…”
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The nonreceptor tyrosine kinase SRMS inhibits autophagy and promotes tumor growth by phosphorylating the scaffolding protein FKBP51 by Park, Jung Mi, Yang, Seung Wook, Zhuang, Wei, Bera, Asim K, Liu, Yan, Gurbani, Deepak, von Hoyningen-Huene, Sergei J, Sakurada, Sadie Miki, Gan, Haiyun, Pruett-Miller, Shondra M, Westover, Kenneth D, Potts, Malia B

“…Nutrient-responsive protein kinases control the balance between anabolic growth and catabolic processes such as autophagy. Aberrant regulation of these kinases…”
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Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis by Shi, Ke, Cho, Seunghee, Aukema, Kelly G, Lee, Thomas, Bera, Asim K, Seffernick, Jennifer L, Wackett, Lawrence P, Aihara, Hideki

“…An ancient enzyme family responsible for the catabolism of the prebiotic chemical cyanuric acid (1,3,5-triazine-2,4,6-triol) was recently discovered and is…”
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KRASQ61H Preferentially Signals through MAPK in a RAF Dimer-Dependent Manner in Non–Small Cell Lung Cancer by Zhou, Zhi-Wei, Ambrogio, Chiara, Bera, Asim K., Li, Qing, Li, Xing-Xiao, Li, Lianbo, Son, Jieun, Gondi, Sudershan, Li, Jiaqi, Campbell, Emily, Jin, Hua, Okoro, Jeffrey J., Xu, Cheng-Xiong, Janne, Pasi A., Westover, Kenneth D.

“…Abstract Assembly of RAS molecules into complexes at the cell membrane is critical for RAS signaling. We previously showed that oncogenic KRAS codon 61…”
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Insights from Analysis of Binding Sites of Human Meprins: Screening of Inhibitors by Molecular Dynamics Simulation Study by Chaudhuri, Ankur, Bera, Asim K, Sarkar, Indrani, Chakraborty, Sibani

“…Human meprin-α and-β are important regulators of angiogenesis, cancer, inflammation, fibrosis, and neurodegenerative diseases and hence important therapeutic…”
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Crystal Structure of the Pyocyanin Biosynthetic Protein PhzS by Greenhagen, Bryan T, Shi, Katherine, Robinson, Howard, Gamage, Swarna, Bera, Asim K, Ladner, Jane E, Parsons, James F

“…The human pathogen Pseudomonas aeruginosa produces pyocyanin, a blue-pigmented phenazine derivative, which is known to play a role in virulence. Pyocyanin is…”
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Structure and Characterization of a Covalent Inhibitor of Src Kinase by Gurbani, Deepak, Du, Guangyan, Henning, Nathaniel J, Rao, Suman, Bera, Asim K, Zhang, Tinghu, Gray, Nathanael S, Westover, Kenneth D

“…Unregulated Src activity promotes malignant processes in cancer, but no Src-directed targeted therapies are used clinically, possibly because early Src…”
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Generalized biomolecular modeling and design with RoseTTAFold All-Atom by Krishna, Rohith, Wang, Jue, Ahern, Woody, Sturmfels, Pascal, Venkatesh, Preetham, Kalvet, Indrek, Lee, Gyu Rie, Morey-Burrows, Felix S, Anishchenko, Ivan, Humphreys, Ian R, McHugh, Ryan, Vafeados, Dionne, Li, Xinting, Sutherland, George A, Hitchcock, Andrew, Hunter, C Neil, Kang, Alex, Brackenbrough, Evans, Bera, Asim K, Baek, Minkyung, DiMaio, Frank, Baker, David

“…Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold…”
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KRAS Switch Mutants D33E and A59G Crystallize in the State 1 Conformation by Lu, Jia, Bera, Asim K, Gondi, Sudershan, Westover, Kenneth D

“…KRAS switch loop movements play a crucial role in regulating RAS signaling, and alteration of these sensitive dynamics is a principal mechanism through which…”
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An enumerative algorithm for de novo design of proteins with diverse pocket structures by Basanta, Benjamin, Bick, Matthew J., Bera, Asim K., Norn, Christoffer, Chow, Cameron M., Carter, Lauren P., Goreshnik, Inna, Dimaio, Frank, Baker, David

“…To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but…”
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Accurate de novo design of membrane-traversing macrocycles by Bhardwaj, Gaurav, O’Connor, Jacob, Rettie, Stephen, Huang, Yen-Hua, Ramelot, Theresa A., Mulligan, Vikram Khipple, Alpkilic, Gizem Gokce, Palmer, Jonathan, Bera, Asim K., Bick, Matthew J., Di Piazza, Maddalena, Li, Xinting, Hosseinzadeh, Parisa, Craven, Timothy W., Tejero, Roberto, Lauko, Anna, Choi, Ryan, Glynn, Calina, Dong, Linlin, Griffin, Robert, van Voorhis, Wesley C., Rodriguez, Jose, Stewart, Lance, Montelione, Gaetano T., Craik, David, Baker, David

“…We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability…”
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Improving Protein Expression, Stability, and Function with ProteinMPNN by Sumida, Kiera H., Núñez-Franco, Reyes, Kalvet, Indrek, Pellock, Samuel J., Wicky, Basile I. M., Milles, Lukas F., Dauparas, Justas, Wang, Jue, Kipnis, Yakov, Jameson, Noel, Kang, Alex, De La Cruz, Joshmyn, Sankaran, Banumathi, Bera, Asim K., Jiménez-Osés, Gonzalo, Baker, David

“…Natural proteins are highly optimized for function but are often difficult to produce at a scale suitable for biotechnological applications due to poor…”
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De novo design of transmembrane β barrels by Vorobieva, Anastassia A, White, Paul, Liang, Binyong, Horne, Jim E, Bera, Asim K, Chow, Cameron M, Gerben, Stacey, Marx, Sinduja, Kang, Alex, Stiving, Alyssa Q, Harvey, Sophie R, Marx, Dagan C, Khan, G Nasir, Fleming, Karen G, Wysocki, Vicki H, Brockwell, David J, Tamm, Lukas K, Radford, Sheena E, Baker, David

“…Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into…”
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Mechanism-Based Inactivation of Benzoylformate Decarboxylase, A Thiamin Diphosphate-Dependent Enzyme by Bera, Asim K, Polovnikova, Lena S, Roestamadji, Juliatek, Widlanski, Theodore S, Kenyon, George L, McLeish, Michael J, Hasson, Miriam S

“…Benzoylformate decarboxylase (BFD) from Pseudomonas putida is a thiamin diphosphate-dependent enzyme that catalyzes the non-oxidative decarboxylation of…”
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Takinib, a Selective TAK1 Inhibitor, Broadens the Therapeutic Efficacy of TNF-α Inhibition for Cancer and Autoimmune Disease by Totzke, Juliane, Gurbani, Deepak, Raphemot, Rene, Hughes, Philip F, Bodoor, Khaldon, Carlson, David A, Loiselle, David R, Bera, Asim K, Eibschutz, Liesl S, Perkins, Marisha M, Eubanks, Amber L, Campbell, Phillip L, Fox, David A, Westover, Kenneth D, Haystead, Timothy A J, Derbyshire, Emily R

“…Tumor necrosis factor alpha (TNF-α) has both positive and negative roles in human disease. In certain cancers, TNF-α is infused locally to promote tumor…”
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