NMR paper High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles.

		BioNMR > Educational resources > Journal club
[NMR paper] High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

02-03-2016, 10:22 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles.

Related Articles High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles.

J Biomol NMR. 2015 Apr;61(3-4):227-34

Authors: Usachev KS, Efimov SV, Kolosova OA, Filippov AV, Klochkov VV

Abstract
PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-?-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel ?-sheet when it binds to DPC micelles.

PMID: 25430060 [PubMed - indexed for MEDLINE]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study Abstract A tendency to dimerize in the presence of lipids was found for the protegrin. The dimer formation by the protegrin-1 (PG-1) is the first step for further oligomeric membrane pore formation. Generally there are two distinct model of PG-1 dimerization in either a parallel or antiparallel β-sheet. But despite the wealth of data available today, protegrin dimer structure and pore formation is still not completely understood....	nmrlearner	Journal club	0	03-19-2015 07:38 AM
High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles Abstract PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12...	nmrlearner	Journal club	0	11-28-2014 11:37 AM
[NMR paper] Use of a combination of the RDC method and NOESY NMR spectroscopy to determine the structure of Alzheimer's amyloid A?10-35 peptide in solution and in SDS micelles. Use of a combination of the RDC method and NOESY NMR spectroscopy to determine the structure of Alzheimer's amyloid A?10-35 peptide in solution and in SDS micelles. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Use of a combination of the RDC method and NOESY NMR spectroscopy to determine the structure of Alzheimer's amyloid A?10-35 peptide in solution and in SDS micelles. Eur Biophys J. 2013 Dec;42(11-12):803-10 Authors: Usachev KS, Filippov AV,...	nmrlearner	Journal club	0	07-06-2014 08:28 PM
[NMR paper] NMR solution structure and condition-dependent oligomerization of the antimicrobial peptide human defensin 5. NMR solution structure and condition-dependent oligomerization of the antimicrobial peptide human defensin 5. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles NMR solution structure and condition-dependent oligomerization of the antimicrobial peptide human defensin 5. Biochemistry. 2012 Dec 4;51(48):9624-37 Authors: Wommack AJ, Robson SA, Wanniarachchi YA, Wan A, Turner CJ, Wagner G, Nolan EM Abstract Human defensin 5 (HD5) is a 32-residue host-defense peptide...	nmrlearner	Journal club	0	03-30-2013 12:59 PM
NMR Solution Structure and Condition-Dependent Oligomerization of the Antimicrobial Peptide Human Defensin 5 NMR Solution Structure and Condition-Dependent Oligomerization of the Antimicrobial Peptide Human Defensin 5 http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi301255u/aop/images/medium/bi-2012-01255u_0008.gif Biochemistry DOI: 10.1021/bi301255u http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/_E-DoepbaP8 More...	nmrlearner	Journal club	0	11-20-2012 04:20 AM
NMR study of the structure and self-association of Core peptide in aqueous solution and DPC micelles. NMR study of the structure and self-association of Core peptide in aqueous solution and DPC micelles. NMR study of the structure and self-association of Core peptide in aqueous solution and DPC micelles. Biopolymers. 2011;96(2):177-80 Authors: Zheng G, Torres AM, Ali M, Manolios N, Price WS Core peptide is a hydrophobic peptide derived from the T-cell antigen receptor-alpha chain (TCR-alpha) transmembrane region with therapeutic potential. The mechanism by which the peptide inserts into the membrane, including any requirements to change...	nmrlearner	Journal club	0	07-20-2011 10:00 AM
[NMR paper] High-resolution molecular structure of a peptide in an amyloid fibril determined by m High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Related Articles High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):711-6 Authors: Jaroniec CP, MacPhee CE, Bajaj VS, McMahon MT, Dobson CM, Griffin RG Amyloid fibrils are self-assembled filamentous structures associated with protein deposition conditions including Alzheimer's disease and the transmissible...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
Oligomeric Structure of a Cathelicidin Antimicrobial Peptide in Dodecylphosphocholine Oligomeric Structure of a Cathelicidin Antimicrobial Peptide in Dodecylphosphocholine Micelle Determined by NMR Spectroscopy. Related Articles Oligomeric Structure of a Cathelicidin Antimicrobial Peptide in Dodecylphosphocholine Micelle Determined by NMR Spectroscopy. Biochim Biophys Acta. 2010 Oct 6; Authors: Saravanan R, Bhattacharjya S The broad spectrum of antibacterial activities of host defense cationic antimicrobial peptides (AMPs) arises from their ability to perturb membrane integrity of the microbes. The mechanisms are often thought to...	nmrlearner	Journal club	0	10-12-2010 02:52 PM

« Previous Thread | Next 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