Modeling and structure determination of homo-oligomeric proteins : an overview of challenges and current approaches

Gaber, Aljaž (author), Pavšič, Miha (author)

Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.

• Language: English
• Keywords: structure determination, modeling, homo-oligomers
• Work type: Article
• Typology: 1.02 - Review Article
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: 21 str.
• Numbering: Vol. 22, iss. 16, art. 9081
• PID: 20.500.12556/RUL-136048
• UDC: 577.112
• ISSN on article: 1422-0067
• DOI: 10.3390/ijms22169081
• COBISS.SI-ID: 73894147
• Publication date in RUL: 08.04.2022

Record is a part of a journal

• Title: International journal of molecular sciences
• Shortened title: Int. j. mol. sci.
• Publisher: MDPI
• ISSN: 1422-0067
• COBISS.SI-ID: 2779162

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 23.08.2021

Secondary language

• Language: Slovenian
• Keywords: določanje strukture, modeliranje, homo-oligomeri