NMR Evidence for Forming Highly Populated Helical Conformations in the Partially Folded hNck2 SH3 Domain  Jingxian Liu, Jianxing Song  Biophysical Journal 

Slides:



Advertisements
Similar presentations
Jean Baum, Barbara Brodsky  Folding and Design 
Advertisements

The Contribution of Entropy, Enthalpy, and Hydrophobic Desolvation to Cooperativity in Repeat-Protein Folding  Tural Aksel, Ananya Majumdar, Doug Barrick 
Volume 86, Issue 5, Pages (May 2004)
Volume 112, Issue 12, Pages (June 2017)
Volume 103, Issue 5, Pages (September 2012)
Solid-State NMR Characterization of Gas Vesicle Structure
Volume 23, Issue 11, Pages (November 2015)
Volume 95, Issue 8, Pages (October 2008)
Volume 3, Issue 5, Pages (October 1998)
Backbone Dynamics of the 18
Volume 13, Issue 5, Pages (May 2005)
Volume 108, Issue 3, Pages (February 2015)
Volume 7, Issue 8, Pages (August 1999)
Volume 95, Issue 1, Pages (July 2008)
Carlos R. Baiz, Andrei Tokmakoff  Biophysical Journal 
Volume 90, Issue 1, Pages (January 2006)
Volume 9, Issue 11, Pages (November 2001)
Volume 109, Issue 4, Pages (August 2015)
Volume 86, Issue 4, Pages (April 2004)
Myosin VI Undergoes Cargo-Mediated Dimerization
James J Chou, Honglin Li, Guy S Salvesen, Junying Yuan, Gerhard Wagner 
De Novo Design of Foldable Proteins with Smooth Folding Funnel
Volume 90, Issue 1, Pages (January 2006)
Volume 105, Issue 3, Pages (August 2013)
Volume 18, Issue 3, Pages (March 2010)
Structure of Bax  Motoshi Suzuki, Richard J. Youle, Nico Tjandra  Cell 
Design and NMR analyses of compact, independently folded BBA motifs
G. Fiorin, A. Pastore, P. Carloni, M. Parrinello  Biophysical Journal 
The Arginine-Rich RNA-Binding Motif of HIV-1 Rev Is Intrinsically Disordered and Folds upon RRE Binding  Fabio Casu, Brendan M. Duggan, Mirko Hennig 
Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif  Bryan T. Martin, Pedro Serrano,
Volume 23, Issue 11, Pages (November 2015)
Volume 23, Issue 5, Pages (May 2015)
Volume 8, Issue 7, Pages (July 2000)
Yusuke Nakasone, Kazunori Zikihara, Satoru Tokutomi, Masahide Terazima 
Volume 95, Issue 1, Pages (July 2008)
Volume 21, Issue 6, Pages (June 2013)
Solution Structure of the RAIDD CARD and Model for CARD/CARD Interaction in Caspase-2 and Caspase-9 Recruitment  James J Chou, Hiroshi Matsuo, Hanjun.
Volume 95, Issue 9, Pages (November 2008)
Volume 17, Issue 7, Pages (July 2009)
Volume 19, Issue 1, Pages (January 2011)
Yuliang Zhang, Yuri L. Lyubchenko  Biophysical Journal 
Volume 106, Issue 4, Pages (February 2014)
Volume 103, Issue 5, Pages (September 2012)
Volume 10, Issue 2, Pages (February 2002)
Scaffolding in the Spliceosome via Single α Helices
Velocity-Dependent Mechanical Unfolding of Bacteriorhodopsin Is Governed by a Dynamic Interaction Network  Christian Kappel, Helmut Grubmüller  Biophysical.
Subdomain Interactions Foster the Design of Two Protein Pairs with ∼80% Sequence Identity but Different Folds  Lauren L. Porter, Yanan He, Yihong Chen,
On Hydrophobicity and Conformational Specificity in Proteins
Volume 102, Issue 10, Pages (May 2012)
Transmuting α helices and β sheets
Solution Structure of a TBP–TAFII230 Complex
Two Latent and Two Hyperstable Polymeric Forms of Human Neuroserpin
Volume 110, Issue 9, Pages (May 2016)
Volume 93, Issue 10, Pages (November 2007)
Volume 8, Issue 7, Pages (July 2000)
NMR Structures of the Second Transmembrane Domain of the Human Glycine Receptor α1 Subunit: Model of Pore Architecture and Channel Gating  Pei Tang, Pravat.
Volume 80, Issue 6, Pages (June 2001)
Volume 110, Issue 11, Pages (June 2016)
Volume 1, Issue 5, Pages R95-R106 (October 1996)
Backbone Dynamics of the 18
Volume 27, Issue 7, Pages e5 (July 2019)
Structure and Interactions of PAS Kinase N-Terminal PAS Domain
Volume 14, Issue 2, Pages (February 2006)
Characterization of Structure, Dynamics, and Detergent Interactions of the Anti-HIV Chemokine Variant 5P12-RANTES  Maciej Wiktor, Oliver Hartley, Stephan.
Volume 25, Issue 9, Pages e3 (September 2017)
Volume 109, Issue 7, Pages (October 2015)
Volume 112, Issue 8, Pages (April 2017)
Kinetic Folding Mechanism of Erythropoietin
Volume 109, Issue 12, Pages (December 2015)
Volume 105, Issue 5, Pages (September 2013)
Presentation transcript:

NMR Evidence for Forming Highly Populated Helical Conformations in the Partially Folded hNck2 SH3 Domain  Jingxian Liu, Jianxing Song  Biophysical Journal  Volume 95, Issue 10, Pages 4803-4812 (November 2008) DOI: 10.1529/biophysj.107.125641 Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 1 Bioinformatics analysis of secondary structures. (a) Three-dimensional structure of first hNck2 SH3 domain determined by NMR spectroscopy (23). (b) Secondary-structure prediction of first hNck2 SH3 domain by computational programs GOR4, PHD, Predator, and SIMPA96. e, β-strand; h, helix; c, random coil. The four residues “LWLL” identified here are highlighted in gray. (c) Bar plots for secondary structure contents, as predicted by GOR4, PHD, Predator, and SIMPA96. Biophysical Journal 2008 95, 4803-4812DOI: (10.1529/biophysj.107.125641) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 2 Far-UV CD characterization of first hNck2 SH3 domain: far-UV CD spectra for wild-type at pH 6.5 (black), wild-type at pH 2.0 (gray), 4AlaMut at pH 6.5 (dotted line), and 4AlaMut at pH 2.0 (dashed line). (Inset) The pH-induced conformational changes of the wild-type as monitored by ellipticity at 222nm. Biophysical Journal 2008 95, 4803-4812DOI: (10.1529/biophysj.107.125641) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 3 The 1H-15N NMR HSQC spectra for different forms of first hNck2 SH3 domain. (a) Wild-type at pH 6.5. (b) Wild-type at pH 2.0. (c) 4AlaMut at pH 6.5. All spectra were acquired on an 800-MHz NMR spectrometer at 278K. Sequential assignments were labeled for all spectra. Biophysical Journal 2008 95, 4803-4812DOI: (10.1529/biophysj.107.125641) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 4 Chemical-shift deviations and helix populations. (a) Bar plot of Cα chemical-shift deviations from their random-coil values for wild-type at pH 6.5 (gray) and pH 2.0 (black). (b) Bar plot of Hα chemical-shift deviations for wild-type at pH 2.0 (black) and 4AlaMut at pH 6.5 (gray). (c) Ratio (× 100) between Hα deviations of wild-type at pH 2.0 (black), 4AlaMut at pH 6.5 (gray), and fully folded but exposed helix residues previously reported (50). Black box indicates mutation region. Secondary-structure fragments are also indicated. Biophysical Journal 2008 95, 4803-4812DOI: (10.1529/biophysj.107.125641) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 5 Characteristic NOEs defining secondary-structure NOE connectivities identified for (a) wild-type at pH 2.0 and (b) 4AlaMut at pH 6.5. Plots were generated by CYANA 2.1 (Güntert, riken, Wako, Saitama, Japan). Biophysical Journal 2008 95, 4803-4812DOI: (10.1529/biophysj.107.125641) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 6 The 15N NMR backbone relaxation data for wild-type at pH 6.5 (yellow), wild-type at pH 2.0 (blue), and 4AlaMut at pH 6.5 (red). (a) {1H}-15N steady-state NOE intensities. (b) 15N T1 (longitudinal) relaxation times. (c) 15N T2 (transverse) relaxation times. All NMR experiments used for deriving these data were recorded at 278K on an 800-MHz Bruker Avance NMR spectrometer. Mutation region is enclosed in red, and secondary-structure fragments are indicated. Biophysical Journal 2008 95, 4803-4812DOI: (10.1529/biophysj.107.125641) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 7 Tertiary packing cores in Src and first hNck2 SH3 domains. (a) Sequence alignment between Src and first hNck2 SH3 domains. (b) Tertiary packing cores in first hNck2 SH3 domain formed by residues Leu25-Trp26-Leu27-Leu28 (yellow) identified in present study and Val37 (red), corresponding to Ala45 reported previously (25). (c) Tertiary packing cores in Src SH3 domain formed by residues Ala45 (red) and Leu32-Gln33-Ile34-Val35 (yellow), corresponding to Leu25-Trp26-Leu27-Leu28 in first Nck2 SH3 domain. Biophysical Journal 2008 95, 4803-4812DOI: (10.1529/biophysj.107.125641) Copyright © 2008 The Biophysical Society Terms and Conditions