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Hashim Al-Hashimi

Research Profile

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Procedures

Nuclear Magnetic Resonance, Biomolecular

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Chemicals & Drugs

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Publications

TOP 3
Evgenia N Nikolova; Charles L Brooks; Garrett B Goh; Hashim M Al-Hashimi
Characterizing the protonation state of Cytosine in transient g·c Hoogsteen base pairs in duplex DNA.
Loïc Salmon; Ioan Andricioaei; Gavin Bascom; Hashim M Al-Hashimi
A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.
Aaron T Frank; Scott Horowitz; Ioan Andricioaei; Hashim M Al-Hashimi
Utility of 1H NMR chemical shifts in determining RNA structure and dynamics.

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All Publications

2013: Evgenia N Nikolova; Charles L Brooks; Garrett B Goh; Hashim M Al-Hashimi
Characterizing the protonation state of Cytosine in transient g·c Hoogsteen base pairs in duplex DNA.
Journal of the American Chemical Society 2013;135(18):6766-9.
2013: Loïc Salmon; Ioan Andricioaei; Gavin Bascom; Hashim M Al-Hashimi
A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.
Journal of the American Chemical Society 2013;135(14):5457-66.
2013: Aaron T Frank; Scott Horowitz; Ioan Andricioaei; Hashim M Al-Hashimi
Utility of 1H NMR chemical shifts in determining RNA structure and dynamics.
The journal of physical chemistry. B 2013;117(7):2045-52.
2012: Elizabeth A Dethoff; Katja Petzold; Anette Casiano-Negroni; Jeetender Chugh; Hashim M Al-Hashimi
Visualizing transient low-populated structures of RNA.
Nature 2012;491(7426):724-8.
2012: Evgenia N Nikolova; Ioan Andricioaei; Gavin D Bascom; Hashim M Al-Hashimi
Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.
Biochemistry 2012;51(43):8654-64.
2012: Lisa E Prevette; Evgenia N Nikolova; Hashim M Al-Hashimi; Mark M Banaszak Holl
Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release.
Molecular pharmaceutics 2012;9(9):2743-9.
2012: Jameson R Bothe; Ky Lowenhaupt; Hashim M Al-Hashimi
Incorporation of CC steps into Z-DNA: interplay between B-Z junction and Z-DNA helical formation.
Biochemistry 2012;51(34):6871-9.
2012: Evgenia N Nikolova; Federico L Gottardo; Hashim M Al-Hashimi
Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution.
Journal of the American Chemical Society 2012;134(8):3667-70.
2012: Elizabeth A Dethoff; Anthony M Mustoe; Jeetender Chugh; Hashim M Al-Hashimi
Functional complexity and regulation through RNA dynamics.
Nature 2012;482(7385):322-30.
2012: Catherine D Eichhorn; Jun Feng; Krishna C Suddala; Nils G Walter; Charles L Brooks; Hashim M Al-Hashimi
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.
Nucleic acids research 2012;40(3):1345-55.
2012: Anthony M Mustoe; Robert M Teixeira; Maximillian H Bailor; Charles L Brooks; Hashim M Al-Hashimi
New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation.
Nucleic acids research 2012;40(2):892-904.
2011: Katja Petzold; Hashim M Al-Hashimi
RNA structure: Adding a second dimension.
Nature chemistry 2011;3(12):913-5.
2011: Jameson R Bothe; Jeetender Chugh; Catherine D Eichhorn; Alexandar L Hansen; Evgenia N Nikolova; Hashim M Al-Hashimi
Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.
Nature methods 2011;8(11):919-31.
2011: Maximillian H Bailor; Charles L Brooks; Anthony M Mustoe; Hashim M Al-Hashimi
3D maps of RNA interhelical junctions.
Nature protocols 2011;6(10):1536-45.
2011: Andrew C Stelzer; Michael D Swanson; Ioan Andricioaei; Aaron T Frank; Marta J Gonzalez-Hernandez; Jeremy D Kratz; Janghyun Lee; David M Markovitz; Hashim M Al-Hashimi
Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble.
Nature chemical biology 2011;7(8):553-9.
2011: Yuta Suzuki; Hashim M Al-Hashimi; Benjamin C Buer; E Neil Marsh
Using fluorine nuclear magnetic resonance to probe changes in the structure and dynamics of membrane-active peptides interacting with lipid bilayers.
Biochemistry 2011;50(27):5979-87.
2011: Maximillian H Bailor; Charles L Brooks; Anthony M Mustoe; Hashim M Al-Hashimi
Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.
Current opinion in structural biology 2011;21(3):296-305.
2011: Scott Horowitz; Joseph D Yesselman; Hashim M Al-Hashimi; Raymond C Trievel
Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9.
The Journal of biological chemistry 2011;286(21):18658-63.
2011: Evgenia N Nikolova; Eunae Kim; Abigail A Wise; Patrick O'Brien; Ioan Andricioaei; Hashim M Al-Hashimi
Transient Hoogsteen base pairs in canonical duplex DNA.
Nature 2011;470(7335):498-502.
2011: Jameson R Bothe; Ky Lowenhaupt; Hashim M Al-Hashimi
Sequence-specific B-DNA flexibility modulates Z-DNA formation.
Journal of the American Chemical Society 2011;133(7):2016-8.
2010: Elizabeth A Dethoff; Hashim M Al-Hashimi
A rare example of lock-and-key RNA recognition.
Journal of molecular biology 2010;404(4):553-4.
2010: Hashim M Al-Hashimi
Biochemistry. Exciting structures.
Science (New York, N.Y.) 2010;329(5997):1295-6.
2010: Evgenia N Nikolova; Hashim M Al-Hashimi
Thermodynamics of RNA melting, one base pair at a time.
RNA (New York, N.Y.) 2010;16(9):1687-91.
2010: Andrew C Stelzer; Jeremy D Kratz; Qi Zhang; Hashim M Al-Hashimi
RNA dynamics by design: biasing ensembles towards the ligand-bound state.
Angewandte Chemie (International ed. in English) 2010;49(33):5731-3.
2010: Benjamin C Buer; Jeetender Chugh; Hashim M Al-Hashimi; E Neil Marsh
Using fluorine nuclear magnetic resonance to probe the interaction of membrane-active peptides with the lipid bilayer.
Biochemistry 2010;49(27):5760-5.
2010: Kristin S Koutmou; Anette Casiano-Negroni; Melissa M Getz; Samuel Pazicni; Andrew J Andrews; James Penner-Hahn; Hashim M Al-Hashimi; Carol A Fierke
NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(6):2479-84.
2010: Catherine Musselman; Qi Zhang; Hashim M Al-Hashimi; Ioan Andricioaei
Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.
The journal of physical chemistry. B 2010;114(2):929-39.
2010: Maximillian H Bailor; Xiaoyan Sun; Hashim M Al-Hashimi
Topology links RNA secondary structure with global conformation, dynamics, and adaptation.
Science (New York, N.Y.) 2010;327(5962):202-6.
2010: Elizabeth A Dethoff; Alexandar L Hansen; Qi Zhang; Hashim M Al-Hashimi
Variable helix elongation as a tool to modulate RNA alignment and motional couplings.
Journal of magnetic resonance (San Diego, Calif. : 1997) 2010;202(1):117-21.
2010: Andrew C Stelzer; Richard W Frazee; Chad Van Huis; Joanne Cleary; Anthony William Opipari Jr; Gary D Glick; Hashim M Al-Hashimi
NMR studies of an immunomodulatory benzodiazepine binding to its molecular target on the mitochondrial F(1)F(0)-ATPase.
Biopolymers 2010;93(1):85-92.
2009: Benjamin C Buer; Roberto de la Salud-Bea; Hashim M Al-Hashimi; E Neil Marsh
Engineering protein stability and specificity using fluorous amino acids: the importance of packing effects.
Biochemistry 2009;48(45):10810-7.
2009: Qi Zhang; Hashim M Al-Hashimi
Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.
RNA (New York, N.Y.) 2009;15(11):1941-8.
2009: Andrew C Stelzer; Aaron T Frank; Maximillian H Bailor; Ioan Andricioaei; Hashim M Al-Hashimi
Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.
Methods (San Diego, Calif.) 2009;49(2):167-73.
2009: Evgenia N Nikolova; Hashim M Al-Hashimi
Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR.
Journal of biomolecular NMR 2009;45(1-2):9-16.
2009: Hashim M Al-Hashimi
Structural biology: Aerial view of the HIV genome.
Nature 2009;460(7256):696-8.
2009: Aaron T Frank; Andrew C Stelzer; Hashim M Al-Hashimi; Ioan Andricioaei
Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.
Nucleic acids research 2009;37(11):3670-9.
2009: Charles K Fisher; Hashim M Al-Hashimi
Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings.
The journal of physical chemistry. B 2009;113(18):6173-6.
2009: Alexandar L Hansen; Evgenia N Nikolova; Anette Casiano-Negroni; Hashim M Al-Hashimi
Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopy.
Journal of the American Chemical Society 2009;131(11):3818-9.
2008: Charles K Fisher; Qi Zhang; Andrew Stelzer; Hashim M Al-Hashimi
Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR.
The journal of physical chemistry. B 2008;112(51):16815-22.
2008: Elizabeth A Dethoff; Alexandar L Hansen; Catherine Musselman; Eric D Watt; Ioan Andricioaei; Hashim M Al-Hashimi
Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.
Biophysical journal 2008;95(8):3906-15.
2008: Hashim M Al-Hashimi; Nils Walter
RNA dynamics: it is about time.
Current opinion in structural biology 2008;18(3):321-9.
2008: Qi Zhang; Hashim M Al-Hashimi
Extending the NMR spatial resolution limit for RNA by motional couplings.
Nature methods 2008;5(3):243-5.
2007: Alexandar L Hansen; Hashim M Al-Hashimi
Dynamics of large elongated RNA by NMR carbon relaxation.
Journal of the American Chemical Society 2007;129(51):16072-82.
2007: Qi Zhang; Andrew C Stelzer; Charles K Fisher; Hashim M Al-Hashimi
Visualizing spatially correlated dynamics that directs RNA conformational transitions.
Nature 2007;450(7173):1263-7.
2007: Hashim M Al-Hashimi
Beyond static structures of RNA by NMR: folding, refolding, and dynamics at atomic resolution.
Biopolymers 2007;86(5-6):345-7.
2007: Melissa Getz; Xiaoyan Sun; Anette Casiano-Negroni; Qi Zhang; Hashim M Al-Hashimi
NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.
Biopolymers 2007;86(5-6):384-402.
2007: Catherine Musselman; Hashim M Al-Hashimi; Ioan Andricioaei
iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.
Biophysical journal 2007;93(2):411-22.
2007: Anette Casiano-Negroni; Xiaoyan Sun; Hashim M Al-Hashimi
Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition.
Biochemistry 2007;46(22):6525-35.
2007: Melissa M Getz; Andy J Andrews; Carol A Fierke; Hashim M Al-Hashimi
Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation.
RNA (New York, N.Y.) 2007;13(2):251-66.
2007: Maximillian H Bailor; Catherine Musselman; Alexandar L Hansen; Kush Gulati; Dinshaw J Patel; Hashim M Al-Hashimi
Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings.
Nature protocols 2007;2(6):1536-46.
2007: Xiaoyan Sun; Qi Zhang; Hashim M Al-Hashimi
Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition.
Nucleic acids research 2007;35(5):1698-713.
2006: Catherine Musselman; Stephen W Pitt; Kush Gulati; Lesley L Foster; Ioan Andricioaei; Hashim M Al-Hashimi
Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings.
Journal of biomolecular NMR 2006;36(4):235-49.
2006: Alexandar L Hansen; Hashim M Al-Hashimi
Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints.
Journal of magnetic resonance (San Diego, Calif. : 1997) 2006;179(2):299-307.
2006: Qi Zhang; Xiaoyan Sun; Eric D Watt; Hashim M Al-Hashimi
Resolving the motional modes that code for RNA adaptation.
Science (New York, N.Y.) 2006;311(5761):653-6.
2006: Hyang-Yeol Lee; Kyung-Hoon Lee; Hashim M Al-Hashimi; E Neil Marsh
Modulating protein structure with fluorous amino acids: increased stability and native-like structure conferred on a 4-helix bundle protein by hexafluoroleucine.
Journal of the American Chemical Society 2006;128(1):337-43.
2005: Hashim M Al-Hashimi
Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy.
Chembiochem : a European journal of chemical biology 2005;6(9):1506-19.
2005: Stephen W Pitt; Qi Zhang; Dinshaw J Patel; Hashim M Al-Hashimi
Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility.
Angewandte Chemie (International ed. in English) 2005;44(22):3412-5.
2004: Stephen W Pitt; Ananya Majumdar; Alexander Serganov; Dinshaw J Patel; Hashim M Al-Hashimi
Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization.
Journal of molecular biology 2004;338(1):7-16.
2003: Qi Zhang; Rachel Throolin; Stephen W Pitt; Alexander Serganov; Hashim M Al-Hashimi
Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment.
Journal of the American Chemical Society 2003;125(35):10530-1.
2003: Hashim M Al-Hashimi; Stephen W Pitt; Ananya Majumdar; Weijun Xu; Dinshaw J Patel
Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings.
Journal of molecular biology 2003;329(5):867-73.
2002: Hashim M Al-Hashimi; Andrey Gorin; Ananya Majumdar; Yuying Gosser; Dinshaw J Patel
Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings.
Journal of molecular biology 2002;318(3):637-49.
2002: Hashim M Al-Hashimi; Yuying Gosser; Andrey Gorin; weidong hu; Ananya Majumdar; Dinshaw J Patel
Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.
Journal of molecular biology 2002;315(2):95-102.
2002: Grant S Heffelfinger; Anthony Martino; Andrey Gorin; Ying Xu; Mark D Rintoul; Al Geist; Hashim M Al-Hashimi; George S Davidson; Jean-Loup Faulon; Laurie J Frink; David M Haaland; William E Hart; Erik Jakobsson; Todd Lane; Ming Li; Phil Locascio; Frank Olken; Victor Olman; Brian Palenik; Steven J Plimpton; Diana C Roe; Nagiza F Samatova; Manesh Shah; Arie Shoshoni; Charlie E M Strauss; Edward V Thomas; Jerilyn A Timlin; Dong Xu
Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.
Omics : a journal of integrative biology 2002;6(4):305-30.
2002: Hashim M Al-Hashimi; Dinshaw J Patel
Residual dipolar couplings: synergy between NMR and structural genomics.
Journal of biomolecular NMR 2002;22(1):1-8.
2001: Hashim M Al-Hashimi; JR Tolman; Ananya Majumdar; Andrey Gorin; Dinshaw J Patel
Determining stoichiometry in homomultimeric nucleic acid complexes using magnetic field induced residual dipolar couplings.
Journal of the American Chemical Society 2001;123(24):5806-7.
2001: Hashim M Al-Hashimi; Andrey Gorin; Ananya Majumdar; Dinshaw J Patel
Alignment of the HTLV-I Rex peptide bound to its target RNA aptamer from magnetic field-induced residual dipolar couplings and intermolecular hydrogen bonds.
Journal of the American Chemical Society 2001;123(13):3179-80.
2001: JR Tolman; Hashim M Al-Hashimi; Lewis E Kay; James H Prestegard
Structural and dynamic analysis of residual dipolar coupling data for proteins.
Journal of the American Chemical Society 2001;123(7):1416-24.
2001: Hashim M Al-Hashimi; Ananya Majumdar; Andrey Gorin; A Kettani; Eugene Skripkin; Dinshaw J Patel
Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation.
Journal of the American Chemical Society 2001;123(4):633-40.
2001: F Tian; Hashim M Al-Hashimi; J L Craighead; James H Prestegard
Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.
Journal of the American Chemical Society 2001;123(3):485-92.
2000: C A Fowler; F Tian; Hashim M Al-Hashimi; James H Prestegard
Rapid determination of protein folds using residual dipolar couplings.
Journal of molecular biology 2000;304(3):447-60.
2000: James H Prestegard; Hashim M Al-Hashimi; JR Tolman
NMR structures of biomolecules using field oriented media and residual dipolar couplings.
Quarterly reviews of biophysics 2000;33(4):371-424.
2000: Hashim M Al-Hashimi; Homayoun Valafar; Mark Terrell; ER Zartler; Marly K Eidsness; James H Prestegard
Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.
Journal of magnetic resonance (San Diego, Calif. : 1997) 2000;143(2):402-6.
2000: Hashim M Al-Hashimi; Pascal Bolon; James H Prestegard
Molecular symmetry as an aid to geometry determination in ligand protein complexes.
Journal of magnetic resonance (San Diego, Calif. : 1997) 2000;142(1):153-8.
1999: Pascal Bolon; Hashim M Al-Hashimi; James H Prestegard
Residual dipolar coupling derived orientational constraints on ligand geometry in a 53 kDa protein-ligand complex.
Journal of molecular biology 1999;293(1):107-15.