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RIC: Research Interest Comparator
Hilmer, Jonathan, Student
Affiliation: Montana State University, Dept of Chemistry
Email: jkhilmer@gmail.com
Home Page: http://www.chemistry.montana.edu/~bbothner/
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Abstract
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Selected Publications
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RIC Statistics
Results - FULL MEDLINE:
Purification and properties of the constituents of the nitrogenase complex from Clostridium pasteurianum.
J P Vandecasteele ... R H Burris
J Bacteriol 1970 Mar; 101(3)794-801.
Score: 0.648
Biophysical comparison of two canine adenoviruses.
R G Marusyk ... U Lundqvist
J Virol 1970 Apr; 5(4)507-12.
Score: 0.637
Inhibition of HeLa cell protein synthesis by the vaccinia virion.
B Moss
J Virol 1968 Oct; 2(10)1028-37.
Score: 0.567
Efficient transcription of a compact nucleoprotein complex isolated from purified simian virus 40 virions.
J N Brady ... N P Salzman
J Virol 1980 Aug; 35(2)371-81.
Score: 0.517
Purification and immunological characterization of the major internal protein of the RD-114 virus.
S Oroszlan ... R V Gilden
Proc Natl Acad Sci U S A 1972 May; 69(5)1211-5.
Score: 0.512
Use of nondefective adenovirus-simian virus 40 hybrids for mapping the simian virus 40 genome.
T J Kelly ... A M Lewis
J Virol 1973 Sep; 12(3)643-52.
Score: 0.507
Early intracellular events in the replication of bacteriophage T4 deoxyribonucleic acid. V. Further studies on the T4 protein-deoxyribonucleic acid complex.
R C Miller ... A W Kozinski
J Virol 1970 Apr; 5(4)490-501.
Score: 0.496
Three-dimensional structure of penicillium chrysogenum virus: a double-stranded RNA virus with a genuine T=1 capsid.
José R Castón ... José L Carrascosa
J Mol Biol 2003 Aug; 331(2)417-31.
Score: 0.471
Complementary approaches to structure determination of icosahedral viruses.
Kelly K Lee ... John E Johnson
Curr Opin Struct Biol 2003 Oct; 13(5)558-69.
Score: 0.459
Electron-paramagnetic-resonance studies on cobalt(II) carbonic anhydrase-sulphonamide complexes.
S A Cockle ... E Grell
Biochem J 1974 Dec; 143(3)703-15.
Score: 0.452
Mechanism of capsid assembly for an icosahedral plant virus.
A Zlotnick ... M J Young
Virology 2000 Nov; 277(2)450-6.
Score: 0.440
Supramolecular assembly dynamics.
Anna V Davis ... Kenneth N Raymond
Proc Natl Acad Sci U S A 2002 Apr; 99(8)4793-6.
Score: 0.435
Structure-function relationships of icosahedral plant viruses.
H S Savithri ... M R Murthy
Arch Virol 1989 ; 109(3-4)153-72.
Score: 0.434
Structural studies on gastroenteritis viruses.
B V Prasad ... M K Estes
Novartis Found Symp 2001 ; 238()26-37; discussion 37-46.
Score: 0.433
In vitro morphology and maturation of lymphocystis virus.
F H Midlige ... R G Malsberger
J Virol 1968 Aug; 2(8)830-5.
Score: 0.430
Crossing the phase boundary to study protein dynamics and function: combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase.
Igor A Kaltashov ... Stephen J Eyles
J Mass Spectrom 2002 Jun; 37(6)557-65.
Score: 0.424
Assembly of the mitochondrial system. Purification of a mitochondrial product of the ATPase.
M F Sierra ... A Tzagoloff
Proc Natl Acad Sci U S A 1973 Nov; 70(11)3155-9.
Score: 0.416
Probing protein dynamics using temperature jump relaxation spectroscopy.
Robert Callender ... R Brian Dyer
Curr Opin Struct Biol 2002 Oct; 12(5)628-33.
Score: 0.404
Chemical characterization and surface orientation of the major glycoprotein of the human erythrocyte membrane.
V T Marchesi ... R E Scott
Proc Natl Acad Sci U S A 1972 Jun; 69(6)1445-9.
Score: 0.402
Genetic control of capsid length in bacteriophage T4. I. Isolation and preliminary description of four new mutants.
A H Doermann ... L Boehner
J Virol 1973 Aug; 12(2)374-85.
Score: 0.402
Solution NMR of supramolecular complexes: providing new insights into function.
Remco Sprangers ... Lewis E Kay
Nat Methods 2007 Sep; 4(9)697-703.
Score: 0.402
DIFFERENCES IN CYSTINE DEPENDENCE AND CHROMATOGRAPHIC BEHAVIOR BETWEEN TWO TYPE 4 ECHOVIRUS STRAINS.
C WALLIS ... J L MELNICK
J Bacteriol 1965 May; 89()1310-3.
Score: 0.397
Early intracellular events in the replication of bacteriophage T4 deoxyribonucleic acid. VI. Newly synthesized proteins in the T4 protein-deoxyribonucleic acid complex.
R C Miller ... P Buckley
J Virol 1970 Apr; 5(4)502-6.
Score: 0.396
Deciphering protein dynamics from NMR data using explicit structure sampling and selection.
Yiwen Chen ... Nikolay V Dokholyan
Biophys J 2007 Oct; 93(7)2300-6.
Score: 0.395
Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses.
V S Reddy ... J E Johnson
Biophys J 1998 Jan; 74(1)546-58.
Score: 0.395
Raman spectroscopy of protein and nucleic acid assemblies.
G J Thomas
Annu Rev Biophys Biomol Struct 1999 ; 28()1-27.
Score: 0.394
Ultrasonic absorption evidence of structural fluctuations in viral capsids.
R Cerf ... L Hirth
Proc Natl Acad Sci U S A 1979 Apr; 76(4)1780-2.
Score: 0.393
High resolution structural studies of complex icosahedral viruses: a brief overview.
Wah Chiu ... Frazer J Rixon
Virus Res 2002 Jan; 82(1-2)9-17.
Score: 0.391
Fillers in the periorbital complex.
J Charlie Finn ... Sueellen Cox
Facial Plast Surg Clin North Am 2007 Feb; 15(1)123-32.
Score: 0.389
Ordered duplex RNA controls capsid architecture in an icosahedral animal virus.
A J Fisher ... J E Johnson
Nature 1993 Jan; 361(6408)176-9.
Score: 0.388
Toward a new paradigm for studying ascidian developmental dynamics.
Nori Satoh
Dev Dyn 2007 Jul; 236(7)1695-7.
Score: 0.382
Leukemia virus activation in chronic allogeneic disease.
M S Hirsch ... R S Schwartz
Proc Natl Acad Sci U S A 1970 Dec; 67(4)1914-7.
Score: 0.380
The birnavirus crystal structure reveals structural relationships among icosahedral viruses.
Fasséli Coulibaly ... Félix A Rey
Cell 2005 Mar; 120(6)761-72.
Score: 0.378
The structure of a putative scaffolding protein of immature poxvirus particles as determined by electron microscopy suggests similarity with capsid proteins of large icosahedral DNA viruses.
Jae-Kyung Hyun ... Alok K Mitra
J Virol 2007 Oct; 81(20)11075-83.
Score: 0.374
Fluorescence techniques for studying protein structure.
M R Eftink
Methods Biochem Anal 1991 ; 35()127-205.
Score: 0.374
Cryoelectron microscopy of icosahedral virus particles.
Wen Jiang ... Wah Chiu
Methods Mol Biol 2007 ; 369()345-64.
Score: 0.373
Molecular dynamics: deciphering the data.
P Dauber-Osguthorpe ... D J Osguthorpe
J Comput Aided Mol Des 1996 Jun; 10(3)177-85.
Score: 0.372
Three-dimensional structure and stoichiometry of Helmintosporium victoriae190S totivirus.
José R Castón ... Said A Ghabrial
Virology 2006 Apr; 347(2)323-32.
Score: 0.371
Essential dynamics from NMR clusters: dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant.
D M van Aalten ... L Joshua-Tor
Methods 1998 Mar; 14(3)318-28.
Score: 0.371
Three-dimensional structure of calicivirus.
B V Prasad ... A W Smith
J Mol Biol 1994 Jul; 240(3)256-64.
Score: 0.370
Attraction within the membrane. Forces behind transmembrane protein folding and supramolecular complex assembly.
Volkhard Helms
EMBO Rep 2002 Dec; 3(12)1133-8.
Score: 0.370
Methods to study protein dynamics and folding by mass spectrometry.
Stephen J Eyles ... Igor A Kaltashov
Methods 2004 Sep; 34(1)88-99.
Score: 0.368
Protein complexes studied by NMR spectroscopy.
A J Wand ... S W Englander
Curr Opin Biotechnol 1996 Aug; 7(4)403-8.
Score: 0.367
Visualization of ordered genomic RNA and localization of transcriptional complexes in rotavirus.
B V Prasad ... M K Estes
Nature 1996 Aug; 382(6590)471-3.
Score: 0.367
The atomic structure of Carnation Mottle Virus capsid protein.
Morgunova EYu ... B K Vainshtein
FEBS Lett 1994 Feb; 338(3)267-71.
Score: 0.367
Self-assembly of polyhedral shells: a molecular dynamics study.
D C Rapaport
Phys Rev E Stat Nonlin Soft Matter Phys 2004 Nov; 70(5 Pt 1)051905.
Score: 0.367
Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions.
Yuko Tsutsui ... Patrick L Wintrode
Curr Med Chem 2007 ; 14(22)2344-58.
Score: 0.366
Molecular recognition by mass spectrometry.
Alessandra Di Tullio ... Francesco De Angelis
J Mass Spectrom 2005 Jul; 40(7)845-65.
Score: 0.365
Structural studies of viruses by electron cryomicroscopy.
M F Schmid ... W Chiu
Arch Virol Suppl 1994 ; 9()523-9.
Score: 0.365
Stability and dynamics of virus capsids described by coarse-grained modeling.
Anton Arkhipov ... Klaus Schulten
Structure 2006 Dec; 14(12)1767-77.
Score: 0.364
Guanine nucleotide-binding activity as an assay for src protein of rat-derived murine sarcoma viruses.
E M Scolnick ... T Y Shih
Proc Natl Acad Sci U S A 1979 Oct; 76(10)5355-9.
Score: 0.364
Component of strain MC29 avian leukosis virus with the property of defectiveness.
R Ishizaki ... J W Beard
J Virol 1971 Dec; 8(6)821-7.
Score: 0.364
Protein-RNA interactions and virus stability as probed by the dynamics of tryptophan side chains.
Andrea T Da Poian ... Jerson L Silva
J Biol Chem 2002 Dec; 277(49)47596-602.
Score: 0.364
Theoretical aspects of virus capsid assembly.
Adam Zlotnick
J Mol Recognit 2005 Nov-Dec; 18(6)479-90.
Score: 0.363
Unraveling the architecture of viruses by high-resolution atomic force microscopy.
Alexander J Malkin ... Alexander McPherson
Methods Mol Biol 2005 ; 292()85-108.
Score: 0.363
Dynamic activation of protein function: a view emerging from NMR spectroscopy.
A J Wand
Nat Struct Biol 2001 Nov; 8(11)926-31.
Score: 0.363
Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation.
Lars Meinhold ... Jeremy C Smith
Phys Rev E Stat Nonlin Soft Matter Phys 2005 Dec; 72(6 Pt 1)061908.
Score: 0.362
Theoretical studies of viral capsid proteins.
D K Phelps ... C B Post
Curr Opin Struct Biol 2000 Apr; 10(2)170-3.
Score: 0.362
Method for measuring microbial growth in rumen content.
D J Walker ... C J Nader
Appl Microbiol 1968 Aug; 16(8)1124-31.
Score: 0.362
Probing single-molecule protein conformational dynamics.
H Peter Lu
Acc Chem Res 2005 Jul; 38(7)557-65.
Score: 0.361
ENZYMATIC VARIANTS OF INFLUENZA VIRUS. III. FUNCTION OF NEURAMINIDASE IN THE VIRAL GROWTH CYCLE.
B L PADGETT ... D L WALKER
J Bacteriol 1964 Feb; 87()363-9.
Score: 0.361
A tiling approach to virus capsid assembly explaining a structural puzzle in virology.
R Twarock
J Theor Biol 2004 Feb; 226(4)477-82.
Score: 0.361
Structural analysis of viral nucleocapsids by subtraction of partial projections.
Ying Zhang ... Michael G Rossmann
J Struct Biol 2007 Feb; 157(2)356-64.
Score: 0.361
Icosahedral models and viruses: a critical evaluation.
H D MAYOR ... J L MELNICK
Science 1962 Aug; 137()613-5.
Score: 0.360
Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR.
Alexander N Volkov ... Marcellus Ubbink
Proc Natl Acad Sci U S A 2006 Dec; 103(50)18945-50.
Score: 0.359
Analysis of protein complexes using mass spectrometry.
Anne-Claude Gingras ... Ruedi Aebersold
Nat Rev Mol Cell Biol 2007 Aug; 8(8)645-54.
Score: 0.359
Lamellar architecture and crystalline transformation in supramolecular complexes of highly-branched polyethyleneimine-octadecanoic acid.
Surong Zhou ... Duanfu Xu
Chem Commun (Camb) 2003 Aug; (15)1932-3.
Score: 0.359
NMR methods for the study of protein structure and dynamics.
L E Kay
Biochem Cell Biol 1997 ; 75(1)1-15.
Score: 0.358
In vitro translation of the Two RNAs of Nodamura virus, a novel mammalian virus with a divided genome.
J F Newman ... R Rueckert
J Virol 1978 Jan; 25(1)78-85.
Score: 0.357
Fungal virus capsids, cytoplasmic compartments for the replication of double-stranded RNA, formed as icosahedral shells of asymmetric Gag dimers.
R H Cheng ... R B Wickner
J Mol Biol 1994 Dec; 244(3)255-8.
Score: 0.357
Solution structure and dynamics of integral membrane proteins by NMR: a case study involving the enzyme PagP.
Peter M Hwang ... Lewis E Kay
Methods Enzymol 2005 ; 394()335-50.
Score: 0.357
To build a virus capsid. An equilibrium model of the self assembly of polyhedral protein complexes.
A Zlotnick
J Mol Biol 1994 Aug; 241(1)59-67.
Score: 0.356
Pressure provides new insights into protein folding, dynamics and structure.
J L Silva ... C A Royer
Trends Biochem Sci 2001 Oct; 26(10)612-8.
Score: 0.356
Assembly of tobacco mosaic virus in vitro: effect of state of polymerization of the protein component.
K E Richards ... R C Williams
Proc Natl Acad Sci U S A 1972 May; 69(5)1121-4.
Score: 0.355
A negative staining-carbon film technique for studying viruses in the electron microscope. I. Preparative procedures for examining icosahedral and filamentous viruses.
R W Horne ... I P Ronchetti
J Ultrastruct Res 1974 Jun; 47(3)361-83.
Score: 0.355
Viruses and life.
Can Med Assoc J 1967 Aug; 97(8)416-7.
Score: 0.354
Icosahedral packing of RNA viral genomes.
Joseph Rudnick ... Robijn Bruinsma
Phys Rev Lett 2005 Jan; 94(3)038101.
Score: 0.352
Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus.
Wen Jiang ... Wah Chiu
Nature 2006 Feb; 439(7076)612-6.
Score: 0.351
Mechanism of capsid maturation in a double-stranded DNA virus.
R Tuma ... G J Thomas
Proc Natl Acad Sci U S A 1998 Aug; 95(17)9885-90.
Score: 0.350
Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs.
T S Baker ... S D Fuller
Microbiol Mol Biol Rev 1999 Dec; 63(4)862-922, table of contents.
Score: 0.350
Protein dynamics from NMR.
L E Kay
Nat Struct Biol 1998 Jul; 5 Suppl()513-7.
Score: 0.349
Techniques for the study of viruses.
F FULTON
Br Med Bull 1953 ; 9(3)186-90.
Score: 0.349
Functional implications of protein-protein interactions in icosahedral viruses.
J E Johnson
Proc Natl Acad Sci U S A 1996 Jan; 93(1)27-33.
Score: 0.347
Developmental sequence and intracellular sites of synthesis of three structural protein antigens of influenza A2 virus.
K Maeno ... E D Kilbourne
J Virol 1970 Feb; 5(2)153-64.
Score: 0.346
Separation and crystallization of T = 3 and T = 4 icosahedral complexes of the hepatitis B virus core protein.
A Zlotnick ... P T Wingfield
Acta Crystallogr D Biol Crystallogr 1999 Mar; 55(Pt 3)717-20.
Score: 0.346
Comparing capsid assembly of primate lentiviruses and hepatitis B virus using cell-free systems.
Jaisri R Lingappa ... Julia E Dooher
Virology 2005 Mar; 333(1)114-23.
Score: 0.346
Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex.
Brian Bothner ... John E Johnson
Virology 2005 Mar; 334(1)17-27.
Score: 0.346
Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings.
Guillaume Bouvignies ... Martin Blackledge
Chemphyschem 2007 Sep; 8(13)1901-9.
Score: 0.346
Finding a needle in a haystack: detection of a small protein (the 12-kDa VP26) in a large complex (the 200-MDa capsid of herpes simplex virus).
F P Booy ... A C Steven
Proc Natl Acad Sci U S A 1994 Jun; 91(12)5652-6.
Score: 0.345
Toward the supramolecular structure of collagen: a molecular dynamics approach.
Susanna Monti ... Chiara Cappelli
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 2005 Jun; 109(22)11389-98.
Score: 0.345
Protein structure and dynamics: an experimental approach.
R L Jones
Biochem Soc Trans 1990 Oct; 18(5)922-3.
Score: 0.345
Supramolecular complexes in photosynthetic bacteria.
P A Loach
Proc Natl Acad Sci U S A 2000 May; 97(10)5016-8.
Score: 0.345
Single-molecule spectroscopy studies of conformational change dynamics in enzymatic reactions.
H Peter Lu
Curr Pharm Biotechnol 2004 Jun; 5(3)261-9.
Score: 0.345
Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures.
S D Benson ... R M Burnett
Cell 1999 Sep; 98(6)825-33.
Score: 0.344
Attaching a spin to a protein - site-directed spin labeling in structural biology.
Aleksander Czogalla ... Aleksander F Sikorski
Acta Biochim Pol 2007 ; 54(2)235-44.
Score: 0.344
Viruses.
L Liljas
Curr Opin Struct Biol 1996 Apr; 6(2)151-6.
Score: 0.342
Visualization of three-dimensional density maps reconstructed from cryoelectron micrographs of viral capsids.
J F Conway ... A C Steven
J Struct Biol 1996 Jan-Feb; 116(1)200-8.
Score: 0.341
Macromolecular complexes as depots for releasable regulatory proteins.
Partho Sarothi Ray ... Paul L Fox
Trends Biochem Sci 2007 Apr; 32(4)158-64.
Score: 0.341
Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35.
Pasi Antero Laurinmäki ... Sarah Jane Butcher
Structure 2005 Dec; 13(12)1819-28.
Score: 0.341
Structural biology of viruses by the combination of electron cryomicroscopy and X-ray crystallography.
Liang Tang ... John E Johnson
Biochemistry 2002 Oct; 41(39)11517-24.
Score: 0.340
Abstract:
The concerted protein motion that is part of a multi-component complex is rarely obvious from the high resolution three-dimensional structure. Protein function is intimately connected to dynamics and therefore knowledge of the frequency, range, and coordination of motion by supramolecular complexes is critical to understanding how they function. My lab uses viruses as a paradigm for studying protein dynamics in supramolecular complexes. Viruses are also timely subjects for health, nanotechnology and bio-defense related research. The life cycle of a typical virus traverses a range of environments. Assembly, maturation, cellular uptake, and genome delivery require numerous structural calisthenics. It is our goal to understand the role of protein dynamics in viral capsid protein function. The extremely large size and icosahedral architecture of virus capsids limit the use of many standard techniques for studying protein motion such as NMR and FRET. To overcome these problems, we employ an array of biophysical techniques to study the solution phase behavior of viruses. Kinetic hydrolysis, an approach being developed in our lab, is a straight-forward and powerful technique for determining the dynamic regions within a single protein or in the context of a multi-component complex. Site-directed chemical labeling using small molecule probes is a complementary method that allows the solvent accessible space of a protein or protein complex to be surveyed.
Keywords extracted from the abstract:
[ eliminated words list ]
Count
Word
2.713
accessible
1.997
allows
1.396
approach
2.589
architecture
2.389
array
2.166
assembly
1.356
behavior
5.962
bio-defense
2.884
biophysical
5.051
calisthenics
2.553
capsid
3.544
capsids
1.428
cellular
1.357
chemical
1.847
complementary
3.385
complex
3.402
complexes
3.218
concerted
2.513
connected
2.090
context
2.508
coordination
1.660
critical
1.557
cycle
1.639
delivery
2.047
determining
1.308
developed
1.992
dynamic
5.099
dynamics
3.133
employ
2.558
environments
Count
Word
2.206
extremely
1.433
frequency
3.504
fret
1.817
genome
2.270
goal
0.783
health
0.994
high
1.960
hydrolysis
3.808
icosahedral
3.385
intimately
2.060
kinetic
1.702
knowledge
4.423
lab
1.907
labeling
1.349
large
1.375
life
2.129
limit
2.056
maturation
1.099
method
1.865
molecule
5.286
motion
8.298
multi-component
2.566
my
3.634
nanotechnology
2.093
nmr
2.104
numerous
2.486
obvious
2.537
overcome
2.542
paradigm
1.478
part
Count
Word
1.363
phase
2.463
powerful
1.913
probes
1.589
problems
3.372
protein
2.750
range
2.326
rarely
1.473
regions
1.284
related
2.003
require
1.975
resolution
1.068
role
1.329
single
2.291
site-directed
1.444
size
1.271
small
1.630
solution
2.385
solvent
1.780
space
1.569
standard
4.680
straight-forward
1.545
structural
1.291
structure
4.689
studying
1.193
subjects
6.780
supramolecular
2.680
surveyed
1.323
technique
2.731
techniques
2.181
three-dimensional
Count
Word
3.012
timely
4.287
traverses
1.983
typical
2.224
understand
1.789
understanding
1.560
uptake
2.363
uses
0.886
using
1.198
viral
2.378
virus
5.233
viruses
RIC Statistics:
Extraction Method: Keyword Count with Lexical Variants Added
Eliminated words list: MedlinePlus List
Similarity Method: Weighted keyword count
Weighting Method: Term Frequency * Inverse Document Frequency
Database: Medline abstracts (1967 - Present)
Publication Type: All
Score Calculation Method: Cosine Similarity Method
Sort by: Score
Submission date and time: 12-18-2007, 15:42:28
Computation time: 00:00:04
Last updated: Tuesday, 18-Dec-2007 15:42:32 CST