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A Survey on π-π Stackings and π-Cations in Prion P
Biochemistry & Pharmacology: Open Access

Biochemistry & Pharmacology: Open Access
Open Access

ISSN: 2167-0501

+44-20-4587-4809

Editorial - (2015) Volume 4, Issue 3

A Survey on π-π Stackings and π-Cations in Prion Protein Structures

Jiapu Zhang1,2*
1Molecular Model Discovery Laboratory, Department of Chemistry & Biotechnology, Faculty of Science, Engineering & Technology, Swinburne University of Technology, Hawthorn Campus, Hawthorn, Victoria 3122, Australia
2Graduate School of Sciences, Information Technology and Engineering & Centre of Informatics and Applied Optimisation, Faculty of Science, The Federation University Australia, Mount Helen Campus, Mount Helen, Ballarat, Victoria 3353, Australia
*Corresponding Author: Jiapu Zhang, Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn Campus, Hawthorn, Victoria 3122, Australia, Tel: +61392145596/+61353276335 Email: ,

Abstract

π-π stackings and π-cations clearly do some contributions to maintain the structural stability of a normal cellular prion protein (PrP). This short article is to do a survey on the π-π stackings and π-cations in all the PrP structures listed in the PDB (www.rcsb.org) Bank. We find the following important π-π stackings: Y218–F175– Y169 (around the β2-α2 loop), Y162–Y128 (linking the two β-strands), F141–Y150– Y157 (in α-helix 1), H187–F198 (linking α-helix 2 and the α2-α3 loop); and we also find the following important π-cations: F141–R208.(N)NH2 (linking the β1-α1 loop and α- helix 3), Y128–R164.(N)NH2–Y169 (linking β-strand 1 and the β2-α2 loop). Thus, for PrPs, there exists a long “π-chain” Y218– F175–Y169–R164–Y128–Y162 covering the β2-α2 loop, and there exists another long “π-chain” R208–Y141–Y150– Y157–F198– H187 covering the α-helix 1. This short article can be acted as a “quick reference card” for PrP protein structure π-interaction studies in laboratories or in theories.

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Keywords: π-π Stackings; π-chains; Prion protein PrP structures; Two long π-chains

π-π and π-cation interactions play an important role in maintaining the structural stability of PrP. In this short article, we consider all the PrP structures listed in the PDB Bank: first we use the Swiss-PdbViewer 4.1.0 (spdbv.vital-it.ch) to relax (i.e. do Energy Minimisation in the use of Steepest Descent - Conjugate Gradients -Steepest Descent optimization methods) all the PrP structures, and then we use Maestro 10.1 2015–1 (Academic use only) (www.schrodinger.com) to find the π interactions see Table 1, where the code in the ( ) bracket is the PBD ID for each PrP species).

Let us denote some notations for a PrP structure: L0 is the N-terminal structured region before the β-strand 1, B1 is β-strand 1, L1 is the loop between B1 and α- helix 1, H1 is the α-helix 1, L2 is the loop between H1 and β-strand 2, B2 is β- strand 2, L3 is the loop between B2 and α-helix 2, H2 is the α-helix 2, L4 is the loop between H2 and α-helix 3, and H3 is the α-helix 3. From Table 1, we may see that there are π-π stackings (Figure 1): Y218–F175–Y169 (linking H3–H2–L3), H187–F198 (linking H2–L4), F141–Y150–Y157 (in H1), Y225–Y226 (in H3), Y162–Y128 (linking B2–B1), etc. From Table 1, we also see the following π-cations (Figure 1): F141– R208.(N) NH2 (linking L1–H3), Y162–L125.(N)N–Y128–R164.(N)NH2–Y169 (linking B2–L0–B1–L3), F198–R156.(N)NH2 (linking L4–L2), H155– R136.(N)NH2 (linking L2– L1), Y127–L125.(N)N (in L0), etc. The above bioinformatics might be acted as a “quick reference card” for PrP protein structure π-interaction studies [1,2].

biochemistry-pharmacology-Some-selected

Figure 1: Some selected π-interactions of PrPs, where the green dashedlines denote the π-π stackings and the orange colored dashed-lines denote the π-cations

Species π-π-stacking π-cation
mousePrP (1AG2) (1XYX) F175–Y218,Y162–Y128,H187–F198
Y169–Y218
F141–R208.(N)NH2
humanPrP (1QLX)
(1QLZ) (1QM0/1/2/3) (2LSB)
  F175–Y218 Y169–R164.(N)NH2 Y128–R164.(N)NH2,F198–R156.(N)NH2, H155–R136.(N)NH2
bovinePrP (1DWY)
(1DWZ) (1DX0/1)
  Y128–R164.(N)NH2
SyrianHamsterPrP (1B10)
(2LH8)
Y169–F175–Y218
Y169–F175–Y218
 
caninePrP (1XYK)    
catPrP (1XYJ)   Y150–R156.(N)NH2
sheepPrP (1UW3) F141–Y150,Y169–F175–Y218  
mousePrP[N174T] (1Y15) F141–Y150,Y169–F175–Y218 Y128–R164.(N)NH2
humanPrP[Q212P]-M129 (2KUN)   H237–R228.(N)NH2
rabbitPrP[S173N]-NMR (2JOH)   Y127–L124.(N)N,Y144–R147.(N)NH2
rabbitPrP[I214V]-NMR (2JOM) H139–Y149 Y148–R155.(N)NH2
rabbitPrP[S170N]-X-ray (4HLS) Y169–F175 F141–R208.(N)NH2
rabbitPrP[S174N]-X-ray (4HMM) Y169–F175 F141–R208.(N)NH2
rabbitPrP[S170N,S174N] (4HMR) Y169–F175 F141–R208.(N)NH2
mousePrP - at 37˚C (2L39)   Y169-R164.(N)NH2
mousePrP[V166A] (2KFO) Y169–F175  
mousePrP[D167S] (2KU5) F175–Y218  
mousePrP[D167S,N173K] (2KU6) F175–Y218,H187–F198  
mousePrP[Y169G] (2L1D) F141–Y150,F175–Y218,Y225–Y226 Y128–R164.(N)NH2
mousePrP[Y169A] (2L40) W145–Y149,H187–F198  
mousePrP[S170N] (2K1O) Y225–Y226  
mousePrP[S170N,N174T] (1Y16)   Y169–R164.(N)NH2
mousePrP[F175A] (2L1E) Y163–Y218 F141–R208.(N)NH2
mousePrP[Y225A,Y226A] (2KFM) Y169–F175–Y218  
mousePrP[Y169A,Y225A,Y226A] (2L1K)    
elkPrP (1XYW) Y169–F175–Y218  
pigPrP (1XYQ)    
bankVolePrP (2K56) Y169–F175–Y218 Y169–R164.(N)NH2
tammarWallabyPrP (2KFL)   F198–R156.(N)NH2
rabbitPrP-NMR (2FJ3) F140–Y149 Y127–L124.(N)N
rabbitPrP-X-ray (3O79) Y169–F175  
horsePrP (2KU4)   F198–R156.(N)NH2
humanPrP-pH7 (1HJM) (1HJN)   H187–F198,Y218–F175–Y169 F141–R208.(N)NH2
humanPrP(118–224) (4N9O) F175–Y218 Y128–R164.(N)NH2
humanPrP-V129 (3HAK) Y225–Y226,F175–Y218 F141–R208.(N)NH2
humanPrP-M166C/E221C (1H0L) F175–Y218–Y169  
humanPrP-M166V (1E1G)
(1E1J)
  Y225–R228.(N)NH2,Y128–L125.(N)N
Y128–L125.(N)N
humanPrP-S170N (1E1P)
(1E1S)
H187–F198
F141–Y150
  T128–R164.(N)NH2
humanPrP-D178N (2K1D) Y128–Y162,Y150–F141– F141–R208.(N)NH2
humanPrP-D178N-M129 (3HEQ) Y225–Y226,F175–Y218  
humanPrP-D178N-V129 (3HJX)    
humanPrP-F198S-M129 (3HES) F175–Y218 F141–R208.(N)NH2
humanPrP-F198S-V129 (3HER) F175–Y218,Y225–Y226  
humanPrP-R200K (1FKC)
(1FO7)
F175–Y218,Y150–Y157
F175–Y218,Y150–Y157
Y162–L125.(N)N
Y162–L125.(N)N
humanPrP-V209M-M129 (2M8T)    
humanPrP-V210I-M129 (2LEJ)
(2LV1)
Y150–Y157
Y225–Y226
H187–R136.(N)NH2
F141–R208.(N)NH2,W99==K101.(N)NZ
humanPrP-E219K-M129 (2LFT) Y157–Y198,F175–Y218  
humanPrP-R220K (1E1U)
(1E1W)
Y225–Y226
Y225–Y226,Y218–F175–Y169
H155–R136.(N)NH2
H155–R136.(N)NH2
chickenPrP (1U3M) Y235–Y238,F148–W156  
turtlePrP (1U5L) F141–W150,Y162–Y188,Y166–F176  
xenopusLeavisPrP (1XU0) Y149–Y153  
sheepPrP-H168 (1XYU) F175–Y218,F141–Y150,H187–F198 Y128–R164.(N)NH2–Y169
ovinePrP-R168 (1Y2S) Y150–Y157,H187–F198  

Table 1: π-π-stackings and π-cations for each (optimized) PrP.

Acknowledgements

This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant numbered VR0063 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government (Australia).

References

  1. Zhang JP (2015) The Hybrid Idea of Optimization Methods Applied to the Energy Minimization of (Prion) Protein Structures. Proceedings of the Workshop on Continuous Optimization: Theory, Methods and Applications, 16–17 April 2015, Ballarat, Australia.
  2. Zhang JP, Wang F, Chatterjee S (2015) Molecular Dynamics Studies on the Buffalo Prion Protein. Accepted by Journal of Biomolecular Structure & Dynam- ics.
Citation: J Zhang (2015) A Survey on π-π Stackings and π-Cations in Prion Protein Structures. Biochem Pharmacol (Los Angel) 4:e175.

Copyright: © 2015 J Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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