Nathan Nicely


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Research Scientist

Duke Human Vaccine Institute

Research Interests:
Nathan Nicely, Ph.D., is a Research Scientist for the Duke Human Vaccine Institute and Director of the Duke University X-ray Crystallography shared resource. His major research interests lie in the structural biology of anti-HIV antibodies and HIV virion coat proteins. He studies the crystal structures of these antibodies with derivatives from the antigenic HIV coat proteins gp120 and gp41 to understand why some of the antibodies neutralize while others do not.
Dr. Nicely received his Ph.D. in Structural and Molecular Biochemistry from NC State University in 2005 with Dr. Carla Mattos studying the topic of Ras subfamily GTPases. He then completed a postdoctoral fellowship with Dr. Al Claiborne in the Center for Structural Biology at Wake Forest University which involved studying a critical enzyme in the coenzyme A biosynthetic pathway of the microbial pathogen Bacillus anthracis. After a brief stint working in computational biology and bioinformatics with the Renaissance Computing Institute at the University of North Carolina, Dr. Nicely came to the Duke Human Vaccine Institute in early 2008 to help complete the construction of the X-ray crystallography facility and to start the Human Vaccine Institute's structural biology program.
The X-ray Crystallography Shared Resource aims to provide professional, high-quality services in solving and analyzing macromolecular crystal structures to laboratories at Duke and beyond. For PIs who already possess crystallographic expertise, this Shared Resource provides instrument access on an easy fee-for-service basis. The Shared Resource has convenient entry points for labs that are interested in expanding their research projects to include structural biology aims from basic methodological advice to full collaboration.
The facility was constructed in mid-2008 and officially opened its doors to the structural biology community in late 2009. Dr. Nicely enjoys putting a significant amount of his time into the day-to-day operations of the crystallography facility, including user training and assistance as well as maintenance of the hardware and software that support the science.
Representative Publications:
Yang G, Holl TM, Liu Y, Li Y, Lu X, Nicely NI, Kepler TB, Alam SM, Liao HX, Cain DW, Spicer L, VandeBerg JL, Haynes BF, Kelsoe G. Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies. J Exp Med. 2013 Feb 11; 210(2): 241-56. Abstract
Liao HX, Bonsignori M, Alam SM, McLellan JS, Tomaras GD, Moody MA, Kozink DM, Hwang KK, Chen X, Tsao CY, Liu P, Lu X, Parks RJ, Montefiori DC, Ferrari G, Pollara J, Rao M, Peachman KK, Santra S, Letvin NL, Karasavvas N, Yang ZY, Dai K, Pancera M, Gorman J, Wiehe K, Nicely NI, Rerks-Ngarm S, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Sinangil F, Kim JH, Michael NL, Kepler TB, Kwong PD, Mascola JR, Nabel GJ, Pinter A, Zolla-Pazner S, Haynes BF. Vaccine induction of antibodies against a structurally heterogeneous site of immune pressure within HIV-1 envelope protein variable regions 1 and 2. Immunity. 2013 Jan 24; 38(1): 176-86. Abstract
Alam SM, Liao HX, Dennison SM, Jaeger F, Parks R, Anasti K, Foulger A, Donathan M, Lucas J, Verkoczy L, Nicely NI, Tomaras GD, Kelsoe G, Chen B, Kepler TB, Haynes BF. Differential reactivity of germ line allelic variants of a broadly neutralizing HIV-1 antibody to a gp41 fusion intermediate conformation. J Virol. 2011 Nov;85(22):11725-31. Abstract
Werner-Allen JW, Lee CJ, Liu P, Nicely NI, Wang S, Greenleaf AL, Zhou P. cis-Proline-mediated Ser(P)5 dephosphorylation by the RNA polymerase II C-terminal domain phosphatase Ssu72. J Biol Chem. 2011 Feb 18;286(7):5717-26. Abstract
Nicely NI, Dennison SM, Spicer L, Scearce RM, Kelsoe G, Ueda Y, Chen H, Liao HX, Alam SM, Haynes BF. Crystal structure of a non-neutralizing antibody to the HIV-1 gp41 membrane-proximal external region. Nat Struct Mol Biol. 2010 Dec;17(12):1492-4. Abstract
Haynes BF, Nicely NI, Alam SM. HIV-1 autoreactive antibodies: are they good or bad for HIV-1 prevention? Nat Struct Mol Biol. 2010 May;17(5):543-5. No abstract available.
Rowan AS, Nicely NI, Cochrane N, Wlassoff WA, Claiborne A, Hamilton CJ. Nucleoside triphosphate mimicry: a sugar triazolyl nucleoside as an ATP-competitive inhibitor of B. anthracis pantothenate kinase. Org Biomol Chem. 2009 Oct 7;7(19):4029-36.Abstract
Milam SL, Nicely NI, Feeney B, Mattos C, Clark AC. Rapid folding and unfolding of Apaf-1 CARD. J Mol Biol. 2007 May 25;369(1):290-304. Abstract
Nicely NI, Parsonage D, Paige C, Newton GL, Fahey RC, Leonardi R, Jackowski S, Mallett TC, Claiborne A. Structure of the type III pantothenate kinase from Bacillus anthracis at 2.0 A resolution: implications for coenzyme A-dependent redox biology.Biochemistry. 2007 Mar 20;46(11):3234-45. Abstract
Nicely NI, Kosak J, de Serrano V, Mattos C. Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap. Structure. 2004 Nov;12(11):2025-36. Abstract