Publications

2023

  1. Karasawa A, Liu H, Quick M, Hendrickson WA, Liu Q. Crystallographic Characterization of Sodium Ions in a Bacterial Leucine/Sodium Symporter. Link.
  2. Koss H, Crawley T, Palmer AG 3rd. Site-based description of R1ρ relaxation in local reference frames. PMID: 36641894. Link.

2022

  1. Anderson JS, Hernández G, LeMaster DM. Molecular Dynamics-Assisted Optimization of Protein NMR Relaxation Analysis J Chem Theory Comput. 2022 Apr 12;18(4):2091-2104. doi: 10.1021/acs.jctc.1c01165. Epub 2022 Mar 4. PMID: 35245056. Link.
  2. Andrews SF, Raab JE, Gorman J, Gillespie RA, Cheung CSF, Rawi R, Cominsky LY, Boyington JC, Creanga A, Shen CH, Harris DR, Olia AS, Nazzari AF, Zhou T, Houser KV, Chen GL, Mascola JR, Graham BS, Kanekiyo M, Ledgerwood JE, Kwong PD, McDermott AB. A single residue in influenza virus H2 hemagglutinin enhances the breadth of the B cell response elicited by H2 vaccination. Nat Med. 2022;28(2):373-382. Link.
  3. Ashraf KU, Nygaard R, Vickery ON, Erramilli SK, Herrera CM, McConville TH, Petrou VI, Giacometti SI, Dufrisne MB, Nosol K, Zinkle AP, Graham CLB, Loukeris M, Kloss B, Skorupinska-Tudek K, Swiezewska E, Roper DI, Clarke OB, Uhlemann AC, Kossiakoff AA, Trent MS, Stansfeld PJ, Mancia F. Structural basis of lipopolysaccharide maturation by the O-antigen ligase. Nature. 2022;604(7905):371-376. Link.
  4. Bhattacharya S, Palillo A. Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1. Protein Sci. 2022 Feb;31(2):498-512. doi: 10.1002/pro.4248. Epub 2021 Dec 16. PMID: 34865273.  Link
  5. Bruni R. High-Throughput Cell-Free Screening of Eukaryotic Membrane Proteins in Lipidic Mimetics. PMID: 35926131. Link.
  6. Bruni R, Laguerre A, Kaminska AM, McSweeney S, Hendrickson WA, Liu Q. High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics. Protein Sci. 2022 Mar;31(3):639-651. doi: 10.1002/pro.4259. Link.
  7. Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Nature. 2022. Link.
  8. Capper MJ, Yang S, Stone AC, Vatansever S, Zilberg G, Mathiharan YK, Habib R, Hutchinson K, Schlessinger A, Mezei M, Osman R, Zhang B, Wacker D. Substrate Binding and Inhibition of the Anion Exchanger 1 Transporter.  2022. [preprint].  Link.
  9. Chang A, Xiang X, Wang J, Lee C, Arakhamia T, Simjanoska M, Wang C, Carlomagno Y, Zhang G, Dhingra S, Thierry M, Perneel J, Heeman B, Forgrave LM, DeTure M, DeMarco ML, Cook CN, Rademakers R, Dickson DW, Petrucelli L, Stowell MHB, Mackenzie IRA, Fitzpatrick AWP. Homotypic fibrillization of TMEM106B across diverse neurodegenerative diseases. Cell. 2022;185(8):1346-1355 e1315. Link.
  10. Chen J, Wang Q, Malone B, Llewellyn E, Pechersky Y, Maruthi K, Eng ET, Perry JK, Campbell EA, Shaw DE, Darst SA. Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex. Nat Struct Mol Biol. 2022;29(3):250-260. Link.
  11. Chua EYD, Mendez JH, Rapp M, Ilca SL, Zi Tan Y, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem. 2022. Link.
  12. Chuang JZ, Yang N, Nakajima N, Otsu W, Fu C, Yang HH, Lee MP, Akbar AF, Badea TC, Guo Z, Nuruzzaman A, Hsu KS, Dunaief JL, Sung CH. Retinal pigment epithelium-specific CLIC4 mutant is a mouse model of dry age-related macular degeneration. Nat Commun. 2022;13(1):374. Link.
  13. Czajka TF, Vance DJ, Davis S, Rudolph MJ, Mantis NJ. Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins. J Biol Chem. 2022 Apr;298(4):101742. doi: 10.1016/j.jbc.2022.101742. Epub 2022 Feb 17. PMID: 35182523. Link.
  14. Daffern N, Nordyke C, Zhang M, Palmer AG 3rd, Straub John E. Dynamical Models of Chemical Exchange in Nuclear Magnetic Resonance Spectroscopy. PMID: 36687382 PMCID: PMC9850547 (available on 2023-07-01). Link.
  15. De Gasperi R, Mo C, Azulai D, Wang Z, Harlow LM, Du Y, Graham Z, Pan J, Liu Xh, Guo L. Numb is required for optimal contraction of skeletal muscle. Journal of Cachexia, Sarcopenia and Muscle. 2022. Link.
  16. Falzone ME, Feng Z, Alvarenga OE, Pan Y, Lee B, Cheng X, Fortea E, Scheuring S, Accardi A. TMEM16 scramblases thin the membrane to enable lipid scrambling. Nature Communications. 2022;13(1):2604. Link.
  17. Frye AM, Ejemel M, Cavacini L, Wang Y, Rudolph MJ, Song R, Mantis NJ. Agglutination of Borreliella burgdorferi by Transmission-Blocking OspA Monoclonal Antibodies and Monovalent Fab Fragments. Infect Immun. 2022 Sep 15;90(9):e0030622. doi: 10.1128/iai.00306-22. Epub 2022 Aug 24. PMID: 36000876. Link.
  18. Georgiev GI, Malonis RJ, Wirchnianski AS, Wessel AW, Jung HS, Cahill SM, Nyakatura EK, Vergnolle O, Dowd KA, Cowburn D, Pierson TC, Diamond MS, Lai JR. Resurfaced ZIKV EDIII nanoparticle immunogens elicit neutralizing and protective responses in vivo. Cell Chem Biol. 2022 Feb 24:S2451-9456(22)00085-X. doi: 10.1016/j.chembiol.2022.02.004. Online ahead of print. PMID: 35231399. Link
  19. Gobeil SMC, Henderson R, Stalls V, Janowska K, Huang X, May A, Speakman M, Beaudoin E, Manne K, Li D, Parks R, Barr M, Deyton M, Martin M, Mansouri K, Edwards RJ, Sempowski GD, Saunders KO, Wiehe K, Williams W, Korber B, Haynes BF, Acharya P. Structural diversity of the SARS-CoV-2 Omicron spike. Link. 2022.
  20. Gorman J, Cheung CS-F, Duan Z, Sun Y, Wang P, Boyington JC, Biju A, Bylund T, Cheng C, Ou L, Stephens T, Tsybovsky Y, Verardi R, Wang S, Yang Y, Zhang B, Zheng C, Zhou T, Mascola JR, Ho DD, Ho M, Kwong PD. Prefusion-Stabilized Lassa Virus Trimer Identifies Neutralizing Nanobodies and Reveals an Apex-Situated Site of Vulnerability. Link2022:2022.2004.2021.488985. [preprint]
  21. Guerra P, Gonzalez-Alamos M, Llauro A, Casanas A, Querol-Audi J, de Pablo PJ, Verdaguer N. Symmetry disruption commits vault particles to disassembly. Sci Adv. 2022;8(6):eabj7795. Link.
  22. Han B, Takvorian PM, Weiss LM. The Function and Structure of the Microsporidia Polar Tube. Exp Suppl. 2022;114:179-213. Link.
  23. Haque HME, Ejemel M, Vance DJ, Willsey G, Rudolph MJ, Cavacini LA, Wang Y, Mantis NJ, Weis DD. Human B Cell Epitope Map of the Lyme Disease Vaccine Antigen, OspA. ACS Infect Dis. 2022 Dec 9;8(12):2515-2528. doi: 10.1021/acsinfecdis.2c00346. Epub 2022 Nov 9. PMID: 36350351. Link.
  24. Howarth GS, McDermott AE. High-Resolution Magic Angle Spinning NMR of KcsA in Liposomes: The Highly Mobile C-Terminus. Biomolecules 12 2022 Aug 15. Link.
  25. Hunter B, Benoit MPMH, Asenjo AB, Doubleday C, Trofimova D, Sosa H, Allingham JS. Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape. Link. 2022. [preprint]
  26. Karasawa A, Andi B, Fuchs MR, Shi W, McSweeney S, Hendrickson WA, Liu Qun. Multi-crystal native-SAD phasing at 5 keV with a helium environment. IUCrJ. 2022 Nov; 9(6). doi: 10.1107/S205225252200971X. Link.
  27. Keeler EG, McDermott. Rotating Frame Relaxation in Magic Angle Spinning Solid State NMR, a Promising Tool for Characterizing Biopolymer Motion. AE Chemical reviews 122 14940-14953 2022 Sep 28. Link.
  28. Kelley K, Raczkowski AM, Klykov O, Jaroenlak P, Bobe D, Kopylov M, Eng ET, Bhabha G, Potter CS, Carragher B, Noble AJ. Waffle Method: A general and flexible approach for improving throughput in FIB-milling. Nat Commun. 2022;13(1):1857. Link.
  29. Kendall AK, Chandra M, Xie B, Wan W, Jackson LP. Improved mammalian retromer cryo-EM structures reveal a new assembly interface. Link. 2022. [preprint]
  30. Kieuvongngam V, Chen J. Structures of the peptidase-containing ABC transporter PCAT1 under equilibrium and nonequilibrium conditions. Proc Natl Acad Sci U S A. 2022;119(4). Link.
  31. Kloss B. Genomics-based strategies toward the identification of a Z-ISO carotenoid biosynthetic enzyme suitable for structural studies. Methods Enzymol. 2022;671:171-205. doi: 10.1016/bs.mie.2021.12.008. 2022 Feb 18. PMID: 35878977.  Link.
  32. Klykov O, Kopylov M, Carragher B, Heck AJR, Noble AJ, Scheltema RA. Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Mol Cell. 2022;82(2):285-303. Link.
  33. Koo CW, Tucci FJ, He Y, Rosenzweig AC. Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Science. 2022;375(6586):1287-1291. Link.
  34. Laughlin ZT, Nandi S, Dey D, Zelinskaya N, Witek MA, Srinivas P, Nguyen HA, Kuiper EG, Comstock LR, Dunham CM, Conn GL. 50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA. Proc Natl Acad Sci U S A. 2022;119(14):e2120352119. Link.
  35. Liang WG, Wijaya J, Wei H, Noble AJ, Mancl JM, Mo S, Lee D, Lin King JV, Pan M, Liu C, Koehler CM, Zhao M, Potter CS, Carragher B, Li S, Tang WJ. Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition. Nat Commun. 2022;13(1):1833. Link.
  36. Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK. Cryo-EM structure of translesion DNA synthesis polymerase zeta with a base pair mismatch. Nat Commun. 2022;13(1):1050. Link.
  37. Malone BF, Perry JK, Olinares PDB, Chen J, Appelby TK, Feng JY, Bilello JP, Ng H, Sotiris J, Ebrahim M, Chua EYD, Mendez JH, Eng ET, Landick R, Chait BT, Campbell EA, Darst SA. Structural basis for substrate selection by the SARS-CoV-2 replicase. Link2022:2022.2005.2020.492815. [preprint]
  38. Martin JA, Palmer AG 3rd. Comparisons of Ribonuclease HI Homologs and Mutants Uncover a Multistate Model for Substrate Recognition. J Am Chem Soc. 2022 Mar 30;144(12):5342-5349. doi: 10.1021/jacs.1c11897. Epub 2022 Mar 21. PMID: 35312304. Link.
  39. Puno MR, Lima CD. Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex. Cell. 2022;185(12):2132-2147 e2126.Link.
  40. Ram S, Bepler T. Few Shot Protein Generation. Preprint arXiv:220401168. 2022. [preprint]Link
  41. Rashid A, Tevlin M, Lu Y, Shaham S. A developmental pathway for epithelial-to-motoneuron transformation in C. elegansLink2022:2022.2005.2027.493712.
  42. Reddy KD, Ciftci D, Scopelliti AJ, Boudker O. The archaeal glutamate transporter homologue GltPh shows heterogeneous substrate binding. Journal of General Physiology. 2022;154(5):e202213131. Link.
  43. Selvakumar P, Fernández-Mariño AI, Khanra N, He C, Paquette AJ, Wang B, Huang R, Smider VV, Rice WJ, Swartz KJ, Meyerson JR. Structures of the T cell potassium channel Kv1.3 with immunoglobulin modulators. Link. 2022. [preprint]
  44. Trinh TKH, Catalano C, Guo Y. Membrane-active Polymers: NCMNP13-x, NCMNP21-x and NCMNP21b-x for Membrane Protein Structural Biology. Link. 2022.
  45. Tsai K, Stojkovic V, Lee DJ, Young ID, Szal T, Klepacki D, Vazquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nat Struct Mol Biol. 2022;29(2):162-171. Link.
  46. Vallese F, Kim K, Yen LY, Johnston JD, Noble AJ, Calì T, Clarke OB. Architecture of the human erythrocyte ankyrin-1 complex. Link. 2022. [preprint].
  47. Wang C, Polovitskaya MM, Delgado BD, Jentsch TJ, Long SB. Gating choreography and mechanism of the human proton-activated chloride channel ASOR. Sci Adv. 2022;8(5):eabm3942. Link.
  48. Wang Q, Kuci D, Bhattacharya S, Hadden-Perilla J, Gupta R. Dynamic regulation of Zn(II) sequestration by calgranulin C. PMID: 36367084 PMCID: PMC9650546 (available on 2023-09-01). Link.
  49. Wasmuth EV, Broeck AV, LaClair JR, Hoover EA, Lawrence KE, Paknejad N, Pappas K, Matthies D, Wang B, Feng W, Watson PA, Zinder JC, Karthaus WR, de la Cruz MJ, Hite RK, Manova-Todorova K, Yu Z, Weintraub ST, Klinge S, Sawyers CL. Allosteric interactions prime androgen receptor dimerization and activation. Link. 2022. [preprint].
  50. Yelshanskaya MV, Patel DS, Kottke CM, Kurnikova MG, Sobolevsky AI. Opening of glutamate receptor channel to subconductance levels. Nature. 2022;605(7908):172-178. Link.
  51. Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH. Structural basis of transcription antitermination by Q?: NusA induces refolding of Q? to form nozzle for RNA polymerase exit channel. bioRxiv. 2022. [preprint]
  52. Yu Y, Li S, Ser Z, Kuang H, Than T, Guan D, Zhao X, Patel Dinshaw J. Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes. Proceedings of the National Academy of Sciences. 2022;119(23):e2202799119. Link.
  53. Zhao Y, Roy K, Vidossich P, Cancedda L, De Vivo M, Forbush B, Cao E. Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide. Nat Commun. 2022;13(1):2747. Link.
  54. Zheng X, Hu Z, Li H, Yang J. Structure of the human cone photoreceptor cyclic nucleotide-gated channel. Nat Struct Mol Biol. 2022;29(1):40-46. Link.
  55. Zheng X, Li H, Hu Z, Su D, Yang J. Structural and functional characterization of an achromatopsia-associated mutation in a phototransduction channel. Commun Biol. 2022;5(1):190. Link.
  56. Zhou T, Chen L, Gorman J, Wang S, Kwon YD, Lin BC, Louder MK, Rawi R, Stancofski ED, Yang Y, Zhang B, Quigley AF, McCoy LE, Rutten L, Verrips T, Weiss RA, Program VRCP, Doria-Rose NA, Shapiro L, Kwong PD. Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure. 2022. Link.
  57. Zimanyi CM, Kopylov M, Potter CS, Carragher B, Eng ET. Broadening access to cryoEM through centralized facilities. Trends Biochem Sci. 2022;47(2):106-116.  Link.

Acknowledgment and Authorship at NYSBC

In addition to usage of instrumentation, investigators at member institutions of NYSBC are afforded support for research activities by NYSBC Scientific Staff. Such support includes courses and workshops organized at NYSBC, which are typically open to all qualified members of a member research group (students, postdoctoral scientists, etc.), as well as basic training and assistance with experiments for individual researchers. Scientific Staff time and resources are necessarily a limited quantity and the latter activities must be balanced to (i) ensure that all member institutions are appropriately served, and (ii) contributions of Scientific Staff, essential for their scientific development and for national recognition of NYSBC, are duly recognized. Individualized interactions between Scientific Staff and investigators on research projects form a continuum from limited engagement with expert users to full participation as collaborators.

The purpose of this document is to clarify when in this continuum, the involvement of Scientific Staff in a project reaches the level for which co-authorship on publications is warranted. Beyond these guidelines, group leaders at member institutions are encouraged to discuss anticipated involvement of Scientific Staff with the appropriate Director at the start of a project using NYSBC resources to anticipate potential authorships (recognizing that the dividing line could change as a project evolves).

NYSBC itself and relevant NYSBC funding sources must be acknowledged in all publications. The language to be utilized in acknowledgments is available on the NYSBC website, under Publications. In addition, individual members of the Scientific Staff should be acknowledged whenever their assistance has been more than de minimus, but not at the level affording co-authorship.

As in all scientific publications, co-authorship for a member of the Scientific Staff is warranted when an individual has made a significant contribution to the scientific work being described. More specifically, the International Committee of Medical Journal Editors (ICMJE) defines the first criteria for authorship to be “substantial contributions to conception and design, acquisition of data, or analysis and interpretation of data”. Scientific staff members meeting this standard may also participate in “drafting the article or revising it critically for important intellectual content”. Approximate criteria to be used in evaluating this standard are provided in the following table, while recognizing that each of these criteria will be met in different ways for the various research activities at NYSBC.

Not Substantial Substantial
Conception and design Provides guidance on latest or most appropriate versions of experimental protocols available at NYSBC Meets with investigators at beginning or during project to develop the experimental protocol to be utilized, when the Staff Member is providing major guidance.
Acquisition of data Provides basic training afforded to all users of NYSBC and gives occasional advice on experimental protocols or provides occasional assistance in acquisition (checking or starting an instrument when user is not at NYSBC for example). Provides continued substantial assistance to a user in setting up experiments or acquires key data on behalf of the user.
Analysis or interpretation of data Confirms to investigator that a given experiment ran successfully by preliminary assessment of data quality Performs more than preliminary data assessment or participates in interpretation of the data towards goals of the investigation.

Principal investigators, who might not actually be present when members of their research groups are using NYSBC resources, are expected to discuss co-authorship issues with their group members (to sensitize them to the importance of this issue) and to discuss any areas of uncertainty with Directors of the appropriate Departments at NYSBC.