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Martin Gruebele
Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States of America

Faculty Member: Structural Biology > Protein Folding [ since 24 February 2003 ]
[ Homepage ] [ Evaluations ]
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http://www.scs.uiuc.edu/mgweb/

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Evaluations

The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation.
Tam S, Spiess C, …, Poirier MA, Frydman J
Nat Struct Mol Biol 2009 Dec 16(12):1279-85 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 8 Mar 2010

Hybridization kinetics is different inside cells.
Schoen I, Krammer H, Braun D
Proc Natl Acad Sci U S A 2009 Dec 22 106(51):21649-54 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 8 Mar 2010

Infrared laser-mediated gene induction in targeted single cells in vivo.
Kamei Y, Suzuki M, …, Funatsu T, Yuba S
Nat Methods 2009 Jan 6(1):79-81 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 25 Jan 2010

Coordinate-dependent diffusion in protein folding.
Best RB, Hummer G
Proc Natl Acad Sci U S A 2009 December 28:Published online before print [full text]
Selected by | Martin Gruebele
Evaluated 14 Jan 2010

Chaperonin overexpression promotes genetic variation and enzyme evolution.
Tokuriki N, Tawfik DS
Nature 2009 Jun 4 459(7247):668-73 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Andrea Mattevi / Petr Capek and Michal Lebl / Alexey Amunts and Nathan Nelson / Robert Bunet and Barrie Wilkinson / Günter Kramer and Bernd Bukau / Martin Gruebele
Evaluated 6 Nov 2009

Imaging chromophores with undetectable fluorescence by stimulated emission microscopy.
Min W, Lu S, …, Holtom GR, Xie XS
Nature 2009 Oct 22 461(7267):1105-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 6 Nov 2009

Dynamics of locking of peptides onto growing amyloid fibrils.
Reddy G, Straub JE, Thirumalai D
Proc Natl Acad Sci U S A 2009 Jul 21 106(29):11948-53 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 21 Aug 2009

Pressure effect on helix-coil transition of an alanine-based peptide: Theoretical analysis.
Yoshidome T, Kinoshita M
Chem Phys Lett 2009 477:211-5 [full text]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 21 Aug 2009

Rapid folding of the prion protein captured by pressure-jump.
Jenkins DC, Pearson DS, …, Geeves MA, Pinheiro TJ
Eur Biophys J 2009 Jun 38(5):625-35 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 6 Jul 2009

Ruggedness in the folding landscape of protein L.
Waldauer SA, Bakajin O, …, Yao S, Lapidus LJ
HFSP J 2008 Dec 2(6):388-95 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 6 Jul 2009

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.
Lange OF, Lakomek NA, …, Griesinger C, de Groot BL
Science 2008 Jun 13 320(5882):1471-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Matthias Buck / Gottfried Otting / Antonio Rosato / Torleif Härd / Moosa Mohammadi / Thomas Szyperski / Simon Ebbinghaus and Martin Gruebele
Evaluated 14 May 2009

Sequence-specific size, structure, and stability of tight protein knots.
Dzubiella J
Biophys J 2009 Feb 96(3):831-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 14 May 2009

Measuring the folding transition time of single RNA molecules.
Lee TH, Lapidus LJ, …, Herschlag D, Chu S
Biophys J 2007 May 1 92(9):3275-83 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Simon Ebbinghaus and Martin Gruebele
Evaluated 30 Jan 2009

Protein dynamical transition does not require protein structure.
He Y, Ku PI, …, Chen JY, Markelz AG
Phys Rev Lett 2008 Oct 24 101(17):178103 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Dr. Simon Ebbinghaus and Martin Gruebele / Angel Garcia
Evaluated 22 Dec 2008

Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin.
Tripathi S, Portman JJ
J Chem Phys 2008 May 28 128(20):205104 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 7 Aug 2008

Are current molecular dynamics force fields too helical?
Best RB, Buchete NV, Hummer G
Biophys J 2008 Jul 95(1):L07-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 7 Aug 2008

Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.
Krukenberg KA, Förster F, …, Sali A, Agard DA
Structure 2008 May 16(5):755-65 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Susan Krueger / Martin Gruebele / Wolfgang Jahnke / Sophie Jackson
Evaluated 5 Jun 2008

Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design.
Amaro RE, Minh DD, …, Li WW, McCammon JA
J Am Chem Soc 2007 Jun 27 129(25):7764-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Jon Zubieta / Martin Gruebele
Evaluated 4 Jun 2008

Heterogeneous and anomalous diffusion inside lipid tubules.
Guo L, Chowdhury P, Fang J, Gai F
J Phys Chem B 2007 Dec 27 111(51):14244-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 27 Mar 2008

An analytical study of the interplay between geometrical and energetic effects in protein folding.
Suzuki Y, Noel JK, Onuchic JN
J Chem Phys 2008 Jan 14 128(2):025101 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 27 Mar 2008

Protein dynamical transition in terahertz dielectric response.
Markelz AG, Knab JR, Chen JY, He Y
Chem Phys Lett 2007 442:413-417 [full text]
Selected by | Martin Gruebele
Evaluated 14 Jan 2008

Effects of zinc binding on the structure and dynamics of the intrinsically disordered protein prothymosin alpha: evidence for metalation as an entropic switch.
Yi S, Boys BL, …, Konermann L, Choy WY
Biochemistry 2007 Nov 13 46(45):13120-30 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 14 Jan 2008

A model for the origin of protein synthesis as coreplicational scanning of nascent RNA.
Yakhnin AV
Orig Life Evol Biosph 2007 Dec 37(6):523-36 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 11 Jan 2008

Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates.
Qi X, Portman JJ
Proc Natl Acad Sci U S A 2007 Jun 26 104(26):10841-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 13 Nov 2007

Metal-ion-dependent GFP emission in vivo by combining a circularly permutated green fluorescent protein with an engineered metal-ion-binding coiled-coil.
Mizuno T, Murao K, …, Oda M, Tanaka T
J Am Chem Soc 2007 Sep 19 129(37):11378-83 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / Martin Gruebele
Evaluated 9 Nov 2007

Threading a peptide through a peptide: protein loops, rotaxanes, and knots.
Blankenship JW, Dawson PE
Protein Sci 2007 Jul 16(7):1249-56 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 25 Sep 2007

Structure-based discovery of an inhibitor of Arf activation by Sec7 domains through targeting of protein-protein complexes.
Viaud J, Zeghouf M, …, Cherfils J, Chavanieu A
Proc Natl Acad Sci U S A 2007 Jun 19 104(25):10370-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 13 Jul 2007

Understanding stochastic simulations of the smallest genetic networks.
Schultz D, Onuchic JN, Wolynes PG
J Chem Phys 2007 Jun 28 126(24):245102 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 11 Jul 2007

Molecular crowding enhances native state stability and refolding rates of globular proteins.
Cheung MS, Klimov D, Thirumalai D
Proc Natl Acad Sci U S A 2005 Mar 29 102(13):4753-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 16 Apr 2007

Coarse-grained strategy for modeling protein stability in concentrated solutions. III: directional protein interactions.
Cheung JK, Shen VK, Errington JR, Truskett TM
Biophys J 2007 Jun 15 92(12):4316-24 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 13 Apr 2007

A driving and coupling "Pac-Man" mechanism for chromosome poleward translocation in anaphase A.
Liu J, Onuchic JN
Proc Natl Acad Sci U S A 2006 Dec 5 103(49):18432-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 15 Feb 2007

Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality.
West DK, Olmsted PD, Paci E
J Chem Phys 2006 Nov 28 125(20):204910 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 19 Dec 2006

Direct observation of thymine dimer repair in DNA by photolyase.
Kao YT, Saxena C, …, Sancar A, Zhong D
Proc Natl Acad Sci U S A 2005 Nov 8 102(45):16128-32 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 17 Nov 2006

Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy.
Heugen U, Schwaab G, …, Leitner DM, Havenith M
Proc Natl Acad Sci U S A 2006 Aug 15 103(33):12301-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 14 Nov 2006

Ultrafast T-jump in water: studies of conformation and reaction dynamics at the thermal limit.
Ma H, Wan C, Zewail AH
J Am Chem Soc 2006 May 17 128(19):6338-40 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 9 Jun 2006

Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy.
Xu J, Plaxco KW, Allen SJ
Protein Sci 2006 May 15(5):1175-81 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 9 Jun 2006

Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins.
Zong C, Papoian GA, Ulander J, Wolynes PG
J Am Chem Soc 2006 Apr 19 128(15):5168-76 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 9 Jun 2006

Design of functional ferritin-like proteins with hydrophobic cavities.
Swift J, Wehbi WA, …, Saven JG, Dmochowski IJ
J Am Chem Soc 2006 May 24 128(20):6611-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Edward Stiefel / Martin Gruebele
Evaluated 9 Jun 2006

Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.
Collins MD, Hummer G, …, Matthews BW, Gruner SM
Proc Natl Acad Sci U S A 2005 Nov 15 102(46):16668-71 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 1 Feb 2006

Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins.
Laurence TA, Kong X, Jäger M, Weiss S
Proc Natl Acad Sci U S A 2005 Nov 29 102(48):17348-53 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 2 Dec 2005

A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments.
Weinkam P, Zong C, Wolynes PG
Proc Natl Acad Sci U S A 2005 Aug 30 102(35):12401-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 19 Oct 2005

Molecular view of hexagonal phase formation in phospholipid membranes.
Marrink SJ, Mark AE
Biophys J 2004 Dec 87(6):3894-900 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 14 Oct 2005

Reaction coordinates and rates from transition paths.
Best RB, Hummer G
Proc Natl Acad Sci U S A 2005 May 10 102(19):6732-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 17 Jun 2005

Early events in the folding of four-helix-bundle heme proteins.
Faraone-Mennella J, Gray HB, Winkler JR
Proc Natl Acad Sci U S A 2005 May 3 102(18):6315-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 16 Jun 2005

Raft lipids as common components of human extracellular amyloid fibrils.
Gellermann GP, Appel TR, …, Diekmann S, Fändrich M
Proc Natl Acad Sci U S A 2005 May 3 102(18):6297-302 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 16 Jun 2005

Release of long-range tertiary interactions potentiates aggregation of natively unstructured alpha-synuclein.
Bertoncini CW, Jung YS, …, Jovin TM, Zweckstetter M
Proc Natl Acad Sci U S A 2005 Feb 1 102(5):1430-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 29 Mar 2005

Determination of barrier heights and prefactors from protein folding rate data.
Plotkin SS
Biophys J 2005 Jun 88(6):3762-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 21 Mar 2005

An anaerobic mitochondrion that produces hydrogen.
Boxma B, de Graaf RM, …, Huynen MA, Hackstein JH
Nature 2005 Mar 3 434(7029):74-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Jacqueline Upcroft / Jeffrey Lawrence / Tracy Palmer / Martin Gruebele / William Martin
Evaluated 18 Mar 2005

Downhill kinetics of biomolecular interface binding: globally connected scenario.
Wang J, Huang W, Lu H, Wang E
Biophys J 2004 Oct 87(4):2187-94 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 7 Dec 2004

Hydrophobic collapse in multidomain protein folding.
Zhou R, Huang X, Margulis CJ, Berne BJ
Science 2004 Sep 10 305(5690):1605-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Matthew Jacobson / D Peter Tieleman / Martin Gruebele
Evaluated 7 Dec 2004

Three-body interactions improve the prediction of rate and mechanism in protein folding models.
Ejtehadi MR, Avall SP, Plotkin SS
Proc Natl Acad Sci U S A 2004 Oct 19 101(42):15088-93 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 7 Dec 2004

Water in protein structure prediction.
Papoian GA, Ulander J, …, Luthey-Schulten Z, Wolynes PG
Proc Natl Acad Sci U S A 2004 Mar 9 101(10):3352-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 27 Oct 2004

Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy.
Ludtke SJ, Chen DH, …, Chuang DT, Chiu W
Structure 2004 Jul 12(7):1129-36 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Henning Stahlberg / Martin Gruebele / Jose Valpuesta
Evaluated 27 Jul 2004

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.
Snow CD, Qiu L, …, Hagen SJ, Pande VS
Proc Natl Acad Sci U S A 2004 Mar 23 101(12):4077-82 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 30 Apr 2004

Folding of A Three-Helix Bundle at the Folding Speed Limit.
Wang T, Zhu Y, Gai F
J Phys Chem B 2004 108:3694-3697 [full text]
Selected by | Martin Gruebele
Evaluated 14 Apr 2004

Folding a protein in a computer: an atomic description of the folding/unfolding of protein A.
García AE, Onuchic JN
Proc Natl Acad Sci U S A 2003 Nov 25 100(24):13898-903 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Victor Munoz / Martin Gruebele
Evaluated 27 Jan 2004

How fast is protein hydrophobic collapse?
Sadqi M, Lapidus LJ, Muñoz V
Proc Natl Acad Sci U S A 2003 Oct 14 100(21):12117-22 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 22 Oct 2003

Dipolar waves map the structure and topology of helices in membrane proteins.
Mesleh MF, Lee S, …, Marassi FM, Opella SJ
J Am Chem Soc 2003 Jul 23 125(29):8928-35 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 13 Oct 2003

Effect of catenation on protein folding stability.
Zhou HX
J Am Chem Soc 2003 Aug 6 125(31):9280-1 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Martin Gruebele
Evaluated 21 Aug 2003

Zipf's law in gene expression.
Furusawa C, Kaneko K
Phys Rev Lett 2003 Feb 28 90(8):088102 [abstract on PubMed] [related articles] [order article]
Selected by | Martin Gruebele
Evaluated 2 Jul 2003

Hammond behavior versus ground state effects in protein folding: evidence for narrow free energy barriers and residual structure in unfolded states.
Sánchez IE, Kiefhaber T
J Mol Biol 2003 Apr 4 327(4):867-84 [abstract on PubMed] [related articles] [order article]
Selected by | Martin Gruebele
Evaluated 29 May 2003

Role of EDEM in the release of misfolded glycoproteins from the calnexin cycle.
Molinari M, Calanca V, …, Lucca P, Paganetti P
Science 2003 Feb 28 299(5611):1397-400 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Martin Gruebele
Evaluated 2 May 2003

Watching proteins fold one molecule at a time.
Rhoades E, Gussakovsky E, Haran G
Proc Natl Acad Sci U S A 2003 Mar 18 100(6):3197-202 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Jan Antosiewicz / Martin Gruebele
Evaluated 25 Apr 2003

Prevention of transthyretin amyloid disease by changing protein misfolding energetics.
Hammarström P, Wiseman RL, Powers ET, Kelly JW
Science 2003 Jan 31 299(5607):713-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Ross Weatherman / Martin Gruebele
Evaluated 3 Mar 2003

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