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2. Insights into the Cross Talk between Effector and Allosteric Lobes of KRAS from Methyl Conformational Dynamics.

Author

Chao, Fa-An, Dharmaiah, Srisathiyanarayanan, Taylor, Troy, Messing, Simon, Gillette, William, Esposito, Dominic, Nissley, Dwight, Byrd, R, Simanshu, Dhirendra, Cornilescu, Gabriel, and Mccormick, Frank

Subjects
Cell Physiological Phenomena, Humans, Molecular Conformation, Neoplasms, Proto-Oncogene Proteins p21(ras), ras Proteins
Abstract

KRAS is the most frequently mutated RAS protein in cancer patients, and it is estimated that about 20% of the cancer patients in the United States carried mutant RAS proteins. To accelerate therapeutic development, structures and dynamics of RAS proteins had been extensively studied by various biophysical techniques for decades. Although 31P NMR studies revealed population equilibrium of the two major states in the active GMPPNP-bound form, more complex conformational dynamics in RAS proteins and oncogenic mutants subtly modulate the interactions with their downstream effectors. We established a set of customized NMR relaxation dispersion techniques to efficiently and systematically examine the ms-μs conformational dynamics of RAS proteins. This method allowed us to observe varying synchronized motions that connect the effector and allosteric lobes in KRAS. We demonstrated the role of conformational dynamics of KRAS in controlling its interaction with the Ras-binding domain of the downstream effector RAF1, the first kinase in the MAPK pathway. This allows one to explain, as well as to predict, the altered binding affinities of various KRAS mutants, which was neither previously reported nor apparent from the structural perspective.

Published
2022

5. The SeaQuest spectrometer at Fermilab

Author

Aidala, CA, Arrington, JR, Ayuso, C, Bowen, BM, Bowen, ML, Bowling, KL, Brown, AW, Brown, CN, Byrd, R, Carlisle, RE, Chang, T, Chang, WC, Chen, A, Chen, JY, Christian, DC, Chu, X, Dannowitz, BP, Daugherity, M, Diefenthaler, M, Dove, J, Durandet, C, El Fassi, L, Erdos, E, Fox, DM, Geesaman, DF, Gilman, R, Goto, Y, Guo, L, Guo, R, Hague, T, Hicks, CR, Holt, RJ, Isenhower, D, Jiang, X, Katich, JM, Kerns, BM, Kinney, ER, Kitts, ND, Klein, A, Kleinjan, D, Kras, J, Kudo, Y, Lin, PJ, Liu, D, Liu, K, Liu, MX, Lorenzon, W, Makins, NCR, Martinez, JD, McClellan, RE, McDonald, B, McGaughey, PL, McNease, SE, Medeiros, MM, Miller, B, Miller, AJ, Miyasaka, S, Miyachi, Y, Mooney, IA, Morton, DH, Nadim, B, Nagai, K, Nakahara, K, Nakano, K, Nara, S, Obata, S, Peng, JC, Prasad, S, Puckett, AJR, Ramson, BJ, Raymond, RS, Reimer, PE, Rubin, JG, Salinas, R, Sanftl, F, Sawada, S, Sawada, T, Scott, MBC, Selensky, LE, Shibata, TA, Shiu, S, Su, D, Tadepalli, AS, Teo, M, Tice, BG, Towell, CL, Towell, RS, Uemura, S, Wang, SG, Watson, S, White, N, Wickes, AB, Wood, MR, Wu, J, Xi, Z, Ye, Z, and Yin, Y

Subjects
SeaQuest, E906, Drell-Yan, Spectrometer, J/psi, Muon, physics.ins-det, nucl-ex, Nuclear & Particles Physics, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Other Physical Sciences
Abstract

The SeaQuest spectrometer at Fermilab was designed to detect oppositely-charged pairs of muons (dimuons) produced by interactions between a 120 GeV proton beam and liquid hydrogen, liquid deuterium and solid nuclear targets. The primary physics program uses the Drell–Yan process to probe antiquark distributions in the target nucleon. The spectrometer consists of a target system, two dipole magnets and four detector stations. The upstream magnet is a closed-aperture solid iron magnet which also serves as the beam dump, while the second magnet is an open aperture magnet. Each of the detector stations consists of scintillator hodoscopes and a high-resolution tracking device. The FPGA-based trigger compares the hodoscope signals to a set of pre-programmed roads to determine if the event contains oppositely-signed, high-mass muon pairs.

Published
2019

8. The SeaQuest Spectrometer at Fermilab

Author

SeaQuest Collaboration, Aidala, C. A., Arrington, J. R., Ayuso, C., Bowen, B. M., Bowen, M. L., Bowling, K. L., Brown, A. W., Brown, C. N., Byrd, R., Carlisle, R. E., Chang, T., Chang, W. -C., Chen, A., Chen, J. -Y., Christian, D. C., Chu, X., Dannowitz, B. P., Daugherity, M., Diefenthaler, M., Dove, J., Durandet, C., Fassi, L. El, Erdos, E., Fox, D. M., Geesaman, D. F., Gilman, R., Goto, Y., Guo, L., Guo, R., Hague, T., Hicks, C. R., Holt, R. J., Isenhower, D., Jiang, X., Katich, J. M., Kerns, B. M., Kinney, E. R., Kitts, N. D., Klein, A., Kleinjan, D., Kras, J., Kudo, Y., Lin, P. -J., Liu, D., Liu, K., Liu, M. X., Lorenzon, W., Makins, N. C. R., Martinez, J. D., McClellan, R. E., McDonald, B., McGaughey, P. L., McNease, S. E., Medeiros, M. M., Miller, B., Miller, A. J., Miyasaka, S., Miyachi, Y., Mooney, I. A., Morton, D. H., Nadim, B., Nagai, K., Nakahara, K., Nakano, K., Nara, S., Obata, S., Peng, J. C., Prasad, S., Puckett, A. J. R., Ramson, B. J., Raymond, R. S., Reimer, P. E., Rubin, J. G., Salinas, R., Sanftl, F., Sawada, S., Sawada, T., Scott, M. B. C., Selensky, L. E., Shibata, T. -A., Shiu, S., Su, D., Tadepalli, A. S., Teo, M., Tice, B. G., Towell, C. L., Towell, R. S., Uemura, S., Wang, S. G., Watson, S., White, N., Wickes, A. B., Wood, M. R., Wu, J., Xi, Z., Ye, Z., and Yin, Y.

Subjects
Physics - Instrumentation and Detectors, Nuclear Experiment
Abstract

The SeaQuest spectrometer at Fermilab was designed to detect oppositely-charged pairs of muons (dimuons) produced by interactions between a 120 GeV proton beam and liquid hydrogen, liquid deuterium and solid nuclear targets. The primary physics program uses the Drell-Yan process to probe antiquark distributions in the target nucleon. The spectrometer consists of a target system, two dipole magnets and four detector stations. The upstream magnet is a closed-aperture solid iron magnet which also serves as the beam dump, while the second magnet is an open aperture magnet. Each of the detector stations consists of scintillator hodoscopes and a high-resolution tracking device. The FPGA-based trigger compares the hodoscope signals to a set of pre-programmed roads to determine if the event contains oppositely-signed, high-mass muon pairs.

Published
2017

13. A Stochastic Quasi-Newton Method for Large-Scale Optimization

Author

Byrd, R. H., Hansen, S. L., Nocedal, J., and Singer, Y.

Subjects
Mathematics - Optimization and Control, Computer Science - Learning, Statistics - Machine Learning
Abstract

The question of how to incorporate curvature information in stochastic approximation methods is challenging. The direct application of classical quasi- Newton updating techniques for deterministic optimization leads to noisy curvature estimates that have harmful effects on the robustness of the iteration. In this paper, we propose a stochastic quasi-Newton method that is efficient, robust and scalable. It employs the classical BFGS update formula in its limited memory form, and is based on the observation that it is beneficial to collect curvature information pointwise, and at regular intervals, through (sub-sampled) Hessian-vector products. This technique differs from the classical approach that would compute differences of gradients, and where controlling the quality of the curvature estimates can be difficult. We present numerical results on problems arising in machine learning that suggest that the proposed method shows much promise.

Published
2014

16. The SeaQuest spectrometer at Fermilab

Author

Aidala, C.A., Arrington, J.R., Ayuso, C., Bowen, B.M., Bowen, M.L., Bowling, K.L., Brown, A.W., Brown, C.N., Byrd, R., Carlisle, R.E., Chang, T., Chang, W.-C., Chen, A., Chen, J.-Y., Christian, D.C., Chu, X., Dannowitz, B.P., Daugherity, M., Diefenthaler, M., Dove, J., Durandet, C., El Fassi, L., Erdos, E., Fox, D.M., Geesaman, D.F., Gilman, R., Goto, Y., Guo, L., Guo, R., Hague, T., Hicks, C.R., Holt, R.J., Isenhower, D., Jiang, X., Katich, J.M., Kerns, B.M., Kinney, E.R., Kitts, N.D., Klein, A., Kleinjan, D., Kras, J., Kudo, Y., Lin, P.-J., Liu, D., Liu, K., Liu, M.X., Lorenzon, W., Makins, N.C.R., Martinez, J.D., McClellan, R.E., McDonald, B., McGaughey, P.L., McNease, S.E., Medeiros, M.M., Miller, B., Miller, A.J., Miyasaka, S., Miyachi, Y., Mooney, I.A., Morton, D.H., Nadim, B., Nagai, K., Nakahara, K., Nakano, K., Nara, S., Obata, S., Peng, J.C., Prasad, S., Puckett, A.J.R., Ramson, B.J., Raymond, R.S., Reimer, P.E., Rubin, J.G., Salinas, R., Sanftl, F., Sawada, S., Sawada, T., Scott, M.B.C., Selensky, L.E., Shibata, T.-A., Shiu, S., Su, D., Tadepalli, A.S., Teo, M., Tice, B.G., Towell, C.L., Towell, R.S., Uemura, S., Wang, S.G., Watson, S., White, N., Wickes, A.B., Wood, M.R., Wu, J., Xi, Z., Ye, Z., and Yin, Y.

Published
2019
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17. Point mutations in Arf1 reveal cooperative effects of the N-terminal extension and myristate for GTPase-activating protein catalytic activity.

Author

Rosenberg Jr., Eric M., Jian, Xiaoying, Soubias, Olivier, Jackson, Rebekah A., Gladu, Erin, Andersen, Emily, Esser, Lothar, Sodt, Alexander J., Xia, Di, Byrd, R. Andrew, and Randazzo, Paul A.

Subjects
GTPASE-activating protein, COOPERATIVE binding (Biochemistry), GUANINE nucleotide exchange factors, CATALYTIC activity, RAS proteins
Abstract

The ADP-ribosylation factors (Arfs) constitute a family of small GTPases within the Ras superfamily, with a distinguishing structural feature of a hypervariable N-terminal extension of the G domain modified with myristate. Arf proteins, including Arf1, have roles in membrane trafficking and cytoskeletal dynamics. While screening for Arf1:small molecule co-crystals, we serendipitously solved the crystal structure of the non-myristoylated engineered mutation [L8K]Arf1 in complex with a GDP analogue. Like wild-type (WT) non-myristoylated Arf1•GDP, we observed that [L8K]Arf1 exhibited an N-terminal helix that occludes the hydrophobic cavity that is occupied by the myristoyl group in the GDP-bound state of the native protein. However, the helices were offset from one another due to the L8K mutation, with a significant change in position of the hinge region connecting the N-terminus to the G domain. Hypothesizing that the observed effects on behavior of the N-terminus affects interaction with regulatory proteins, we mutated two hydrophobic residues to examine the role of the N-terminal extension for interaction with guanine nucleotide exchange factors (GEFs) and GTPase Activating Proteins (GAPs. Different than previous studies, all mutations were examined in the context of myristoylated Arf. Mutations had little or no effect on spontaneous or GEF-catalyzed guanine nucleotide exchange but did affect interaction with GAPs. [F13A]myrArf1 was less than 1/2500, 1/1500, and 1/200 efficient as substrate for the GAPs ASAP1, ARAP1 and AGAP1; however, [L8A/F13A]myrArf1 was similar to WT myrArf1. Using molecular dynamics simulations, the effect of the mutations on forming alpha helices adjacent to a membrane surface was examined, yet no differences were detected. The results indicate that lipid modifications of GTPases and consequent anchoring to a membrane influences protein function beyond simple membrane localization. Hypothetical mechanisms are discussed. [ABSTRACT FROM AUTHOR]

Published
2024
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26. An Unusual Topological Structure of the HIV-1 Rev Response Element

Author

Fang, Xianyang, Wang, Jinbu, O’Carroll, Ina P., Mitchell, Michelle, Zuo, Xiaobing, Wang, Yi, Yu, Ping, Liu, Yu, Rausch, Jason W., Dyba, Marzena A., Kjems, Jørgen, Schwieters, Charles D., Seifert, Soenke, Winans, Randall E., Watts, Norman R., Stahl, Stephen J., Wingfield, Paul T., Byrd, R. Andrew, Le Grice, Stuart F.J., Rein, Alan, and Wang, Yun-Xing

Published
2013
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38. COMPTEL as a Solar Gamma Ray and Neutron Detector

Author

Ryan, J. M., Aarts, H., Bennett, K., Byrd, R., de Vries, C., den Herder, J. W., Deerenberg, A., Diehl, R., Eymann, G., Forrest, D. J., Foster, C., Hermsen, W., Lockwood, J., Lichti, G., Macri, J., McConnell, M., Morris, D., Schönfelder, V., Simpson, G., Snelling, M., Steinle, H., Strong, A., Swanenburg, B. N., Taddeucci, T., Webber, W. R., Winkler, C., Zichichi, Antonino, editor, Di Gesù, V., editor, Scarsi, L., editor, Buccheri, R., editor, Crane, P., editor, Maccarone, M. C., editor, and Zimmermann, H. U., editor

Published
1992
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40. A structurally conserved site in AUP1 binds the E2 enzyme UBE2G2 and is essential for ER-associated degradation

Author

Smith, Christopher E., primary, Tsai, Yien Che, additional, Liang, Yu-He, additional, Khago, Domarin, additional, Mariano, Jennifer, additional, Li, Jess, additional, Tarasov, Sergey G., additional, Gergel, Emma, additional, Tsai, Borong, additional, Villaneuva, Matthew, additional, Clapp, Michelle E., additional, Magidson, Valentin, additional, Chari, Raj, additional, Byrd, R. Andrew, additional, Ji, Xinhua, additional, and Weissman, Allan M., additional

Published
2021
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45. A simple protocol for the production of highly deuterated proteins for biophysical studies.

Author

Jess Li and Byrd, R. Andrew

Subjects
*ELECTRON paramagnetic resonance spectroscopy, *SPIN labels, *RECOMBINANT proteins
Abstract

Highly deuterated protein samples expand the biophysics and biological tool kit by providing, among other qualities, contrast matching in neutron diffraction experiments and reduction of dipolar spin interactions from normally protonated proteins in magnetic resonance studies, impacting both electron paramagnetic resonance and NMR spectroscopy. In NMR applications, deuteration is often combined with other isotopic labeling patterns to expand the range of conventional NMR spectroscopy research in both solution and solid-state conditions. However, preparation of deuterated proteins is challenging. We present here a simple, effective, and userfriendly protocol to produce highly deuterated proteins in Escherichia coli cells. The protocol utilizes the common shaker flask growth method and the well-known pET system (which provides expression control via the T7 promotor) for largescale recombinant protein expression. One liter expression typically yields 5 to 50 mg of highly deuterated protein. Our data demonstrate that the optimized procedure produces a comparable quantity of protein in deuterium (²H2O) oxide M9 medium compared with that in ¹H2O M9 medium. The protocol will enable a broader utilization of deuterated proteins in a number of biophysical techniques. [ABSTRACT FROM AUTHOR]

Published
2022
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