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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 06-23-2018, 02:31 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy.

Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy.

Related Articles Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy.

Acc Chem Res. 2018 Jun 22;:

Authors: Goldberga I, Li R, Duer MJ

Abstract
The extracellular matrix of a tissue is as important to life as the cells within it. Its detailed molecular structure defines the environment of a tissue's cells and thus their properties, including differentiation and metabolic status. Collagen proteins are the major component of extracellular matrices. Self-assembled collagen fibrils provide both specific mechanical properties to handle external stresses on tissues and, at the molecular level, well-defined protein binding sites to interact with cells. How the cell-matrix interactions are maintained against the stresses on the tissue is an important and as yet unanswered question. Similarly, how collagen molecular and fibrillar structures change in aging and disease is a crucial open question. Solid-state NMR spectroscopy offers insight into collagen molecular conformation in intact in vivo and in vitro tissues, and in this Account we review how NMR spectroscopy is beginning to provide answers to these questions. In vivo 13C,15N labeling of the extracellular matrix has given insight into collagen molecular dynamics and generated multidimensional NMR "fingerprints" of collagen molecular structure that allow comparison of local collagen conformation between tissues. NMR studies have shown that charged collagen residues (Lys, Arg) adopt extended-side-chain conformations in the fibrillar structure to facilitate charge-charge interactions between neighboring collagen molecules, while hydrophobic residues (Leu, Ile) fold along the collagen molecular axis to minimize the hydrophobic area exposed to surrounding water. Detailed NMR and molecular modeling work has shown that the abundant Gly-Pro-Hyp (Hyp = hydroxyproline) triplets in collagen triple helices confer well-defined flexibility because the proline is conformationally metastable, in contrast to the expectation that these triplets confer structural rigidity. The alignment of the Gly-Pro-Hyp triplets within the fibril structure means that the Gly-Pro-Hyp molecular flexibility generates fibril flexibility. The fibrillar bands of Gly-Pro-Hyp are highly correlated with collagen ligand binding sites, leading to the hypothesis that the fibril alignment of Gly-Pro-Hyp triplets is essential to protect collagen-ligand binding against external stresses on the tissue. Non-enzymatic chemistry between collagen side-chain amine groups (Lys, Arg) and reducing sugars-glycation-is an important source of matrix structural change in aging and disease. Glycation leads to stiffening of collagen fibrils, which is widely speculated to be the result of intermolecular cross-linking. The chemistry of non-enzymatic glycation has been extensively detailed through NMR studies and has been shown to lead to side-chain modifications as the majority reaction products, rather than intermolecular cross-links, with resultant molecular misalignment in the fibrils. Thus, a picture is beginning to emerge in which collagen glycation causes stiffening through misalignment of collagen molecular flexible regions rather than intermolecular cross-linking, meaning that new thinking is needed on how to alleviate collagen structural changes in aging and disease.


PMID: 29931970 [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] NMR Insights into the Structure-Function Relationships in the Binding of Melanocortin Analogues to the MC1R Receptor.
NMR Insights into the Structure-Function Relationships in the Binding of Melanocortin Analogues to the MC1R Receptor. Related Articles NMR Insights into the Structure-Function Relationships in the Binding of Melanocortin Analogues to the MC1R Receptor. Molecules. 2017 Jul 15;22(7): Authors: Morais M, Zamora-Carreras H, Raposinho PD, Oliveira MC, Pantoja-Uceda D, Correia JDG, Jiménez MA Abstract Linear and cyclic analogues of the ?-melanocyte stimulating hormone (?-MSH) targeting the human melanocortin receptor 1 (MC1R) are of...
nmrlearner Journal club 0 04-07-2018 03:55 PM
[NMR paper] Direct Evidence of Imino Acid-Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy.
Direct Evidence of Imino Acid-Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy. Related Articles Direct Evidence of Imino Acid-Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy. J Phys Chem Lett. 2014 Nov 20;5(22):4044-8 Authors: Singh C, Rai RK, Aussenac F, Sinha N Abstract Aromatic amino acids (AAAs) have rare presence (~1.4% abundance of Phe) inside of collagen protein, which is the most abundant animal protein playing a functional role in...
nmrlearner Journal club 0 08-16-2015 07:01 PM
Direct Evidence of Imino Acid–Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy
From The DNP-NMR Blog: Direct Evidence of Imino Acid–Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy Singh, C., et al., Direct Evidence of Imino Acid–Aromatic Interactions in Native Collagen Protein by DNP-Enhanced Solid-State NMR Spectroscopy. The Journal of Physical Chemistry Letters, 2014. 5(22): p. 4044-4048. http://dx.doi.org/10.1021/jz502081j
nmrlearner News from NMR blogs 0 11-24-2014 04:15 PM
[NMR paper] Characterization of membrane protein function by solid-state NMR spectroscopy.
Characterization of membrane protein function by solid-state NMR spectroscopy. Characterization of membrane protein function by solid-state NMR spectroscopy. Curr Opin Struct Biol. 2014 Apr 25;27C:48-55 Authors: Baker LA, Baldus M Abstract Membrane proteins are an important class of biological molecules whose association with lipid bilayers and intrinsic molecular mobility can complicate their structural study by high-resolution methods. As different experimental techniques require different membrane mimetics, it can be...
nmrlearner Journal club 0 05-29-2014 09:35 PM
Characterization of membrane protein function by solid-state NMR spectroscopy
Characterization of membrane protein function by solid-state NMR spectroscopy Publication date: August 2014 Source:Current Opinion in Structural Biology, Volume 27</br> Author(s): Lindsay A Baker , Marc Baldus</br> Membrane proteins are an important class of biological molecules whose association with lipid bilayers and intrinsic molecular mobility can complicate their structural study by high-resolution methods. As different experimental techniques require different membrane mimetics, it can be challenging to relate membrane protein structure to function. This...
nmrlearner Journal club 0 05-25-2014 06:31 PM
[NMR paper] Cationic membrane peptides: atomic-level insight of structure-activity relationships from solid-state NMR.
Cationic membrane peptides: atomic-level insight of structure-activity relationships from solid-state NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Cationic membrane peptides: atomic-level insight of structure-activity relationships from solid-state NMR. Amino Acids. 2013 Mar;44(3):821-33 Authors: Su Y, Li S, Hong M Abstract Many membrane-active peptides, such as cationic cell-penetrating peptides (CPPs) and antimicrobial peptides...
nmrlearner Journal club 0 08-15-2013 07:45 PM
[NMR paper] Structure-function relationships in human epidermal growth factor studied by site-dir
Structure-function relationships in human epidermal growth factor studied by site-directed mutagenesis and 1H NMR. Related Articles Structure-function relationships in human epidermal growth factor studied by site-directed mutagenesis and 1H NMR. Biochemistry. 1991 Sep 10;30(36):8891-8 Authors: Hommel U, Dudgeon TJ, Fallon A, Edwards RM, Campbell ID In order to elucidate the mechanism of interaction between human epidermal growth factor (EGF) and its receptor, selected variants of EGF, differing by single amino acid substitutions, have been...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Structure-function relationships in human epidermal growth factor studied by site-dir
Structure-function relationships in human epidermal growth factor studied by site-directed mutagenesis and 1H NMR. Related Articles Structure-function relationships in human epidermal growth factor studied by site-directed mutagenesis and 1H NMR. Biochemistry. 1991 Sep 10;30(36):8891-8 Authors: Hommel U, Dudgeon TJ, Fallon A, Edwards RM, Campbell ID In order to elucidate the mechanism of interaction between human epidermal growth factor (EGF) and its receptor, selected variants of EGF, differing by single amino acid substitutions, have been...
nmrlearner Journal club 0 08-21-2010 11:12 PM



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 - 2024, 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 12:48 PM.


Map