Literature DB >> 26213415

A Newcomer's Guide to Peptide Crystallography.

Ryan K Spencer1, James S Nowick1.   

Abstract

Here we provide a guide for adapting the tools developed for protein X-ray crystallography to study the structures and supramolecular assembly of peptides. Peptide crystallography involves selecting a suitable peptide, crystallizing the peptide, collecting X-ray diffraction data, processing the diffraction data, determining the crystallographic phases and generating an electron density map, building and refining models, and depositing the crystallographic structure in the Protein Data Bank (PDB). Advances in technology make this process easy for a newcomer to adopt. This paper describes techniques for determining the X-ray crystallographic structures of peptides: incorporation of amino acids containing heavy atoms for crystallographic phase determination, commercially available kits to crystallize peptides, modern techniques for X-ray crystallographic data collection, and free user-friendly software for data processing and producing a crystallographic structure.

Entities:  

Keywords:  X-ray crystallography; amino acids; peptide crystallography; peptides; proteins

Year:  2015        PMID: 26213415      PMCID: PMC4508863          DOI: 10.1002/ijch.201400179

Source DB:  PubMed          Journal:  Isr J Chem        ISSN: 0021-2148            Impact factor:   3.333


  36 in total

1.  The Protein Data Bank.

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Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Out-of-register β-sheets suggest a pathway to toxic amyloid aggregates.

Authors:  Cong Liu; Minglei Zhao; Lin Jiang; Pin-Nan Cheng; Jiyong Park; Michael R Sawaya; Anna Pensalfini; Dawei Gou; Arnold J Berk; Charles G Glabe; James Nowick; David Eisenberg
Journal:  Proc Natl Acad Sci U S A       Date:  2012-12-03       Impact factor: 11.205

3.  Novel approach to phasing proteins: derivatization by short cryo-soaking with halides.

Authors:  Z Dauter; M Dauter; K R Rajashankar
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-02

4.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

5.  The site-specific incorporation of p-iodo-L-phenylalanine into proteins for structure determination.

Authors:  Jianming Xie; Lei Wang; Ning Wu; Ansgar Brock; Glen Spraggon; Peter G Schultz
Journal:  Nat Biotechnol       Date:  2004-09-19       Impact factor: 54.908

6.  Structures of oligomers of a peptide from β-amyloid.

Authors:  Johnny D Pham; Nicholas Chim; Celia W Goulding; James S Nowick
Journal:  J Am Chem Soc       Date:  2013-08-08       Impact factor: 15.419

Review 7.  Scaling and assessment of data quality.

Authors:  Philip Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

8.  Better models by discarding data?

Authors:  K Diederichs; P A Karplus
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-15

9.  How good are my data and what is the resolution?

Authors:  Philip R Evans; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-13

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

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  13 in total

1.  Controlling the Oligomerization State of Aβ-Derived Peptides with Light.

Authors:  Patrick J Salveson; Sepehr Haerianardakani; Alexander Thuy-Boun; Adam G Kreutzer; James S Nowick
Journal:  J Am Chem Soc       Date:  2018-04-20       Impact factor: 15.419

2.  Phenylalanine Mutation to Cyclohexylalanine Facilitates Triangular Trimer Formation by β-Hairpins Derived from Aβ.

Authors:  Sepehr Haerianardakani; Adam G Kreutzer; Patrick J Salveson; Tuan D Samdin; Gretchen E Guaglianone; James S Nowick
Journal:  J Am Chem Soc       Date:  2020-11-25       Impact factor: 15.419

Review 3.  Elucidating the Structures of Amyloid Oligomers with Macrocyclic β-Hairpin Peptides: Insights into Alzheimer's Disease and Other Amyloid Diseases.

Authors:  Adam G Kreutzer; James S Nowick
Journal:  Acc Chem Res       Date:  2018-03-06       Impact factor: 22.384

4.  X-ray Crystallographic Structure of a Compact Dodecamer from a Peptide Derived from Aβ16-36.

Authors:  Patrick J Salveson; Ryan K Spencer; Adam G Kreutzer; James S Nowick
Journal:  Org Lett       Date:  2017-06-15       Impact factor: 6.005

5.  X-ray Crystallographic Structures of Oligomers of Peptides Derived from β2-Microglobulin.

Authors:  Ryan K Spencer; Adam G Kreutzer; Patrick J Salveson; Hao Li; James S Nowick
Journal:  J Am Chem Soc       Date:  2015-05-12       Impact factor: 15.419

6.  Total synthesis reveals atypical atropisomerism in a small-molecule natural product, tryptorubin A.

Authors:  Solomon H Reisberg; Yang Gao; Allison S Walker; Eric J N Helfrich; Jon Clardy; Phil S Baran
Journal:  Science       Date:  2020-01-02       Impact factor: 47.728

7.  Synthesis and study of macrocyclic β-hairpin peptides for investigating amyloid oligomers.

Authors:  Gretchen Guaglianone; Adam G Kreutzer; James S Nowick
Journal:  Methods Enzymol       Date:  2021-05-24       Impact factor: 1.682

8.  X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an Aβ17-36 β-Hairpin.

Authors:  Adam G Kreutzer; Imane L Hamza; Ryan K Spencer; James S Nowick
Journal:  J Am Chem Soc       Date:  2016-03-29       Impact factor: 15.419

9.  X-ray Crystallographic Structure of Oligomers Formed by a Toxic β-Hairpin Derived from α-Synuclein: Trimers and Higher-Order Oligomers.

Authors:  Patrick J Salveson; Ryan K Spencer; James S Nowick
Journal:  J Am Chem Soc       Date:  2016-03-23       Impact factor: 15.419

10.  Stabilization, Assembly, and Toxicity of Trimers Derived from Aβ.

Authors:  Adam G Kreutzer; Stan Yoo; Ryan K Spencer; James S Nowick
Journal:  J Am Chem Soc       Date:  2017-01-10       Impact factor: 15.419

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