BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 04-09-2015, 03:47 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,910
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp - Trp Interactions in Designed ?-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for ?-Hairpin Capping.

NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp - Trp Interactions in Designed ?-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for ?-Hairpin Capping.

Related Articles NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp - Trp Interactions in Designed ?-Hairpin Peptides: Terminal Switch from L- to D-Amino Acid as a Strategy for ?-Hairpin Capping.

J Phys Chem B. 2015 Apr 7;

Authors: Makwana KM, Mahalakshmi R

Abstract
Interaction among the side chains of aromatic amino acids is a well-known mechanism of protein and peptide structure stabilization, particularly in ?-sheets. Using short ?-hairpin models bearing the sequence Ac-Leu-Xxx-Val-(D)Pro-Gly-Leu-Trp-Val-NH2, we report the surprising observation of significant destabilization in aryl-tryptophan interactions, which results in poorly folded peptide populations, accompanied by lowering of stability. We find that such destabilization arises from forced occupancy of the indole ring in the shielded 'Edge' position, in T-shaped aryl geometries. We demonstrate that this destabilizing effect can be efficiently salvaged by replacing the N-terminal (L)Leu to (D)Leu, which causes an increase in the folded hairpin population, whilst retaining Trp in the 'Edge' position. Our observation of unique cross strand NOEs, and data from temperature-dependent NMR and CD measurements, reveals the formation of a locally stabilized aliphatic-aromatic network, leading to an overall increase in ?G(0)F by ~ -0.6 to -1.2 kcal/mol. Our results suggest that a contextual evaluation of stabilization by tryptophan is necessary in ?-hairpins. Furthermore, we report for the first time, that the use of D-isomers of aliphatic amino acids at the terminus is stabilizing, which can serve as a new strategy for increasing ?-hairpin stability.


PMID: 25849307 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Nature of aryl-tyrosine interactions contribute to ?-hairpin scaffold stability: NMR evidence for alternate ring geometry.
Nature of aryl-tyrosine interactions contribute to ?-hairpin scaffold stability: NMR evidence for alternate ring geometry. Nature of aryl-tyrosine interactions contribute to ?-hairpin scaffold stability: NMR evidence for alternate ring geometry. Phys Chem Chem Phys. 2015 Jan 8; Authors: Makwana KM, Mahalakshmi R Abstract The specific contribution of the acidic-aromatic ?-sheet favouring amino acid tyrosine to the stability of short octapeptide ?-hairpin structures is presented here. Solution NMR analysis in near-apolar...
nmrlearner Journal club 0 01-09-2015 03:58 PM
Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA)
Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA) Abstract The use of paramagnetic constraints in protein NMR is an active area of research because of the benefits of long-range distance measurements (>10*?). One of the main issues in successful execution is the incorporation of a paramagnetic metal ion into diamagnetic proteins. The most common metal ion tags are relatively long aliphatic chains attached to the side chain of a...
nmrlearner Journal club 0 11-28-2014 11:37 AM
[NMR paper] Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy.
Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy. Related Articles Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy. Biochim Biophys Acta. 2013 Oct 29; Authors: Pope A, Eilers M, Reeves PJ, Smith SO Abstract Rhodopsin is a classical two-state G protein-coupled receptor (GPCR). In the dark, its 11-cis retinal chromophore serves as an inverse agonist to lock the receptor in an inactive state. Retinal-protein and protein-protein...
nmrlearner Journal club 0 11-05-2013 06:53 PM
[NMR paper] NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide.
NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded ?-sheet peptide. J Phys Chem B. 2012 Dec 13;116(49):14207-15 Authors: Sonti R, Rai R, Ragothama S, Balaram P Abstract Cross strand aromatic interactions between a facing pair of...
nmrlearner Journal club 0 06-13-2013 06:14 PM
Analysis of the amide 15N chemical shift tensor of the Cα tetrasubstituted constituent of membrane-active peptaibols, the α-aminoisobutyric acid residue, compared to those of di- and tri-substituted proteinogenic amino acid residues
Analysis of the amide 15N chemical shift tensor of the Cα tetrasubstituted constituent of membrane-active peptaibols, the α-aminoisobutyric acid residue, compared to those of di- and tri-substituted proteinogenic amino acid residues <div class="Abstract">Abstract In protein NMR spectroscopy the chemical shift provides important information for the assignment of residues and a first structural evaluation of dihedral angles. Furthermore, angular restraints are obtained from oriented samples by solution and solid-state NMR spectroscopic approaches. Whereas the anisotropy of chemical...
nmrlearner Journal club 0 01-09-2011 12:46 PM
[NMR paper] An NMR study on the beta-hairpin region of barnase.
An NMR study on the beta-hairpin region of barnase. Related Articles An NMR study on the beta-hairpin region of barnase. Fold Des. 1996;1(3):231-41 Authors: Neira JL, Fersht AR BACKGROUND: The beta-hairpin of barnase (residues Ser92-Leu95) has been proposed in theoretical and protein engineering studies to be an initiation site for folding . There is evidence for residual structure in this region from NMR studies of the denatured protein under different denaturing conditions . A more detailed analysis is possible by NMR studies of isolated...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Proton NMR and structural features of a 24-nucleotide RNA hairpin.
Proton NMR and structural features of a 24-nucleotide RNA hairpin. Related Articles Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry. 1995 May 16;34(19):6488-503 Authors: Borer PN, Lin Y, Wang S, Roggenbuck MW, Gott JM, Uhlenbeck OC, Pelczer I The three-dimensional conformation of a 24-nucleotide variant of the RNA binding sequence for the coat protein of bacteriophage R17 has been analyzed using NMR, molecular dynamics, and energy minimization. The imino proton spectrum is consistent with base pairing...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] An NMR study of the HIV-1 TAR element hairpin.
An NMR study of the HIV-1 TAR element hairpin. Related Articles An NMR study of the HIV-1 TAR element hairpin. Biochemistry. 1993 Nov 23;32(46):12522-30 Authors: Jaeger JA, Tinoco I The TAR hairpin is an important part of the 5' long terminal repeat of HIV-1 and appears to be recognized by a cellular protein. A 14-base model of the native TAR hairpin 5'-GAGC-GCUC-3' (loop bases in square brackets) has been studied by proton, phosphorus, and natural abundance carbon NMR; these results are compared to other published NMR studies of the TAR...
nmrlearner Journal club 0 08-22-2010 03:01 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2020, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 05:59 AM.


Map