Rodolfo Ghirlando, Ph.D.


A selection of recent and significant publications can be viewed below.

Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.
Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish Yadav KN, Feng H, Wang R, Zhang P, Zhurkin V, Bai Y.
J Mol Biol (2018 Sep 14) 430:3093-3110. Abstract/Full Text
The oligomerization state of bacterial enzyme I (EI) determines EI's allosteric stimulation or competitive inhibition by α-ketoglutarate.
Nguyen TT, Ghirlando R, Venditti V.
J Biol Chem (2018 Feb 16) 293:2631-2639. Abstract/Full Text
Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N.
Chittori S, Hong J, Saunders H, Feng H, Ghirlando R, Kelly AE, Bai Y, Subramaniam S.
Science (2018 Jan 19) 359:339-343. Abstract/Full Text
Tilted, Uninterrupted, Monomeric HIV-1 gp41 Transmembrane Helix from Residual Dipolar Couplings.
Chiliveri SC, Louis JM, Ghirlando R, Baber JL, Bax A.
J Am Chem Soc (2018 Jan 10) 140:34-37. Abstract/Full Text
Chemical and Biophysical Approaches for Complete Characterization of Lectin-Carbohydrate Interactions.
Lusvarghi S, Ghirlando R, Davison JR, Bewley CA.
Methods Enzymol (2018) 598:3-35. Abstract/Full Text
Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.
Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C.
Genes Dev (2017 Oct 1) 31:1958-1972. Abstract/Full Text
Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase.
Verardi R, Kim JS, Ghirlando R, Banerjee A.
Structure (2017 Sep 5) 25:1337-1347.e6. Abstract/Full Text
Sirt1 carboxyl-domain is an ATP-repressible domain that is transferrable to other proteins.
Kang H, Oka S, Lee DY, Park J, Aponte AM, Jung YS, Bitterman J, Zhai P, He Y, Kooshapur H, Ghirlando R, Tjandra N, Lee SB, Kim MK, Sadoshima J, Chung JH.
Nat Commun (2017 May 15) 8:15560. Abstract/Full Text
The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2.
Jha JK, Li M, Ghirlando R, Miller Jenkins LM, Wlodawer A, Chattoraj D.
MBio (2017 Apr 18) 8. Abstract/Full Text
Confinement and Stabilization of Fyn SH3 Folding Intermediate Mimetics within the Cavity of the Chaperonin GroEL Demonstrated by Relaxation-Based NMR.
Libich DS, Tugarinov V, Ghirlando R, Clore GM.
Biochemistry (2017 Feb 21) 56:903-906. Abstract/Full Text
Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.
Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis D.
Science (2017 Jan 6) 355:89-92. Abstract/Full Text
Binding Site Geometry and Subdomain Valency Control Effects of Neutralizing Lectins on HIV-1 Viral Particles.
Lusvarghi S, Lohith K, Morin-Leisk J, Ghirlando R, Hinshaw JE, Bewley CA.
ACS Infect Dis (2016 Nov 11) 2:882-891. Abstract/Full Text
Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.
Dharmaiah S, Bindu L, Tran TH, Gillette WK, Frank PH, Ghirlando R, Nissley DV, Esposito D, McCormick F, Stephen AG, Simanshu DK.
Proc Natl Acad Sci U S A (2016 Nov 1) 113:E6766-E6775. Abstract/Full Text
Transient HIV-1 Gag-protease interactions revealed by paramagnetic NMR suggest origins of compensatory drug resistance mutations.
Deshmukh L, Louis JM, Ghirlando R, Clore GM.
Proc Natl Acad Sci U S A (2016 Nov 1) 113:12456-12461. Abstract/Full Text
A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome.
Zhou BR, Feng H, Ghirlando R, Li S, Schwieters CD, Bai Y.
J Mol Biol (2016 Oct 9) 428:3948-3959. Abstract/Full Text
Quantitative Resolution of Monomer-Dimer Populations by Inversion Modulated DEER EPR Spectroscopy.
Schmidt T, Ghirlando R, Baber J, Clore GM.
Chemphyschem (2016 Oct 5) 17:2987-2991. Abstract/Full Text
'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7.
Almawi AW, Matthews LA, Larasati, Myrox P, Boulton S, Lai C, Moraes T, Melacini G, Ghirlando R, Duncker BP, Guarné A.
Sci Rep (2016 Sep 29) 6:34237. Abstract/Full Text
Insights into the Conformation of the Membrane Proximal Regions Critical to the Trimerization of the HIV-1 gp41 Ectodomain Bound to Dodecyl Phosphocholine Micelles.
Louis JM, Baber JL, Ghirlando R, Aniana A, Bax A, Roche J.
PLoS One (2016) 11:e0160597. Abstract/Full Text
CTCF: making the right connections.
Ghirlando R, Felsenfeld G.
Genes Dev (2016 Apr 15) 30:881-91. Abstract/Full Text
Enrichment and characterization of ferritin for nanomaterial applications.
Ghirlando R, Mutskova R, Schwartz C.
Nanotechnology (2016 Jan 29) 27:045102. Abstract/Full Text
Farnesylated and methylated KRAS4b: high yield production of protein suitable for biophysical studies of prenylated protein-lipid interactions.
Gillette WK, Esposito D, Abreu Blanco M, Alexander P, Bindu L, Bittner C, Chertov O, Frank PH, Grose C, Jones JE, Meng Z, Perkins S, Van Q, Ghirlando R, Fivash M, Nissley DV, McCormick F, Holderfield M, Stephen AG.
Sci Rep (2015 Nov 2) 5:15916. Abstract/Full Text
Hfqs in Bacillus anthracis: Role of protein sequence variation in the structure and function of proteins in the Hfq family.
Vrentas C, Ghirlando R, Keefer A, Hu Z, Tomczak A, Gittis AG, Murthi A, Garboczi DN, Gottesman S, Leppla SH.
Protein Sci (2015 Nov) 24:1808-19. Abstract/Full Text
Structural Mechanisms of Nucleosome Recognition by Linker Histones.
Zhou BR, Jiang J, Feng H, Ghirlando R, Xiao TS, Bai Y.
Mol Cell (2015 Aug 20) 59:628-38. Abstract/Full Text
Variable-Field Analytical Ultracentrifugation: I. Time-Optimized Sedimentation Equilibrium.
Ma J, Metrick M, Ghirlando R, Zhao H, Schuck P.
Biophys J (2015 Aug 18) 109:827-37. Abstract/Full Text
G Protein-Coupled Receptor Kinase 2 (GRK2) and 5 (GRK5) Exhibit Selective Phosphorylation of the Neurotensin Receptor in Vitro.
Inagaki S, Ghirlando R, Vishnivetskiy SA, Homan KT, White JF, Tesmer JJ, Gurevich VV, Grisshammer R.
Biochemistry (2015 Jul 21) 54:4320-9. Abstract/Full Text
Successive Stages of Amyloid-β Self-Assembly Characterized by Solid-State Nuclear Magnetic Resonance with Dynamic Nuclear Polarization.
Potapov A, Yau WM, Ghirlando R, Thurber KR, Tycko R.
J Am Chem Soc (2015 Jul 1) 137:8294-307. Abstract/Full Text
A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation.
Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TM, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JG, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BD, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT 4th, Tripathy A, Uchiyama S, Uebel SF, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P.
PLoS One (2015) 10:e0126420. Abstract/Full Text
Glycopeptide mimetics recapitulate high-mannose-type oligosaccharide binding and function.
Lusvarghi S, Ghirlando R, Wong CH, Bewley CA.
Angew Chem Int Ed Engl (2015 May 4) 54:5603-8. Abstract/Full Text
Complete dissociation of the HIV-1 gp41 ectodomain and membrane proximal regions upon phospholipid binding.
Roche J, Louis JM, Aniana A, Ghirlando R, Bax A.
J Biomol NMR (2015 Apr) 61:235-48. Abstract/Full Text
Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy.
Deshmukh L, Ghirlando R, Clore GM.
Proc Natl Acad Sci U S A (2015 Mar 17) 112:3374-9. Abstract/Full Text
Measurement of the temperature of the resting rotor in analytical ultracentrifugation.
Ghirlando R, Zhao H, Balbo A, Piszczek G, Curth U, Brautigam CA, Schuck P.
Anal Biochem (2014 Aug 1) 458:37-9. Abstract/Full Text
Improved measurement of the rotor temperature in analytical ultracentrifugation.
Zhao H, Balbo A, Metger H, Clary R, Ghirlando R, Schuck P.
Anal Biochem (2014 Apr 15) 451:69-75. Abstract/Full Text
The catalytic subunit of the SWR1 remodeler is a histone chaperone for the H2A.Z-H2B dimer.
Hong J, Feng H, Wang F, Ranjan A, Chen J, Jiang J, Ghirlando R, Xiao TS, Wu C, Bai Y.
Mol Cell (2014 Feb 6) 53:498-505. Abstract/Full Text
Investigation of the structure and dynamics of the capsid-spacer peptide 1-nucleocapsid fragment of the HIV-1 gag polyprotein by solution NMR spectroscopy.
Deshmukh L, Ghirlando R, Clore GM.
Angew Chem Int Ed Engl (2014 Jan 20) 53:1025-8. Abstract/Full Text
Initiator protein dimerization plays a key role in replication control of Vibrio cholerae chromosome 2.
Jha JK, Ghirlando R, Chattoraj DK.
Nucleic Acids Res (2014) 42:10538-49. Abstract/Full Text
Physical chemistry of nucleic acids and their complexes.
Ghirlando R, Felsenfeld G.
Biopolymers (2013 Dec) 99:910-5. Abstract/Full Text
Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41.
Gustchina E, Li M, Ghirlando R, Schuck P, Louis JM, Pierson J, Rao P, Subramaniam S, Gustchina A, Clore GM, Wlodawer A.
PLoS One (2013) 8:e78187. Abstract/Full Text
Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states.
Sugiman-Marangos SN, Peel JK, Weiss YM, Ghirlando R, Junop MS.
Nucleic Acids Res (2013 Nov) 41:9934-44. Abstract/Full Text
Structure and dynamics of full-length HIV-1 capsid protein in solution.
Deshmukh L, Schwieters CD, Grishaev A, Ghirlando R, Baber JL, Clore GM.
J Am Chem Soc (2013 Oct 30) 135:16133-47. Abstract/Full Text
Improving the thermal, radial, and temporal accuracy of the analytical ultracentrifuge through external references.
Ghirlando R, Balbo A, Piszczek G, Brown PH, Lewis MS, Brautigam CA, Schuck P, Zhao H.
Anal Biochem (2013 Sep 1) 440:81-95. Abstract/Full Text
Recorded scan times can limit the accuracy of sedimentation coefficients in analytical ultracentrifugation.
Zhao H, Ghirlando R, Piszczek G, Curth U, Brautigam CA, Schuck P.
Anal Biochem (2013 Jun 1) 437:104-8. Abstract/Full Text
A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C.
Kato H, Jiang J, Zhou BR, Rozendaal M, Feng H, Ghirlando R, Xiao TS, Straight AF, Bai Y.
Science (2013 May 31) 340:1110-3. Abstract/Full Text
Chromatin structure outside and inside the nucleus.
Ghirlando R, Felsenfeld G.
Biopolymers (2013 Apr) 99:225-32. Abstract/Full Text
Engineering anthrax toxin variants that exclusively form octamers and their application to targeting tumors.
Phillips DD, Fattah RJ, Crown D, Zhang Y, Liu S, Moayeri M, Fischer ER, Hansen BT, Ghirlando R, Nestorovich EM, Wein AN, Simons L, Leppla SH, Leysath CE.
J Biol Chem (2013 Mar 29) 288:9058-65. Abstract/Full Text
Biophysical characterization of membrane proteins in nanodiscs.
Inagaki S, Ghirlando R, Grisshammer R.
Methods (2013 Mar) 59:287-300. Abstract/Full Text
Identification of functionally conserved regions in the structure of the chaperone/CenH3/H4 complex.
Hong J, Feng H, Zhou Z, Ghirlando R, Bai Y.
J Mol Biol (2013 Feb 8) 425:536-45. Abstract/Full Text
Overview of current methods in sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation.
Zhao H, Brautigam CA, Ghirlando R, Schuck P.
Curr Protoc Protein Sci (2013 Feb) Chapter 20:Unit20.12. Abstract/Full Text
Structural basis for enzyme I inhibition by α-ketoglutarate.
Venditti V, Ghirlando R, Clore GM.
ACS Chem Biol (2013) 8:1232-40. Abstract/Full Text
The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease.
Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F.
Nucleic Acids Res (2012 Oct) 40:9964-79. Abstract/Full Text