NDLI: Simulations of reversible protein aggregate and crystal structure.

Content Provider	PubMed Central
Author	Patro, S. Y. Przybycien, T. M.
Abstract	We simulated the structure of reversible protein aggregates as a function of protein surface characteristics, protein-protein interaction energies, and the entropic penalty accompanying the immobilization of protein in a solid phase. These simulations represent an extension of our previous work on kinetically irreversible protein aggregate structure and are based on an explicit accounting of the specific protein-protein interactions that occur within reversible aggregates and crystals. We considered protein monomers with a mixture of hydrophobic and hydrophilic surface regions suspended in a polar solvent; the energetic driving force for aggregation is provided by the burial of solvent-exposed hydrophobic surface area. We analyzed the physical properties of the generated aggregates, including density, protein-protein contact distributions, solvent accessible surface area, porosity, and order, and compared our results with the protein crystallization literature as well as with the kinetically irreversible case. The physical properties of reversible aggregates were consonant with those observed for the irreversible aggregates, although in general, reversible aggregates were more stable energetically and were more crystal-like in their order content than their irreversible counterparts. The reversible aggregates were less dense than the irreversible aggregates, indicating that the increased energetic stability is derived primarily from the optimality rather than the density of the packing in the solid phase. The extent of hydrophobic protein-protein contacts and solvent-exposed surface area within the aggregate phase depended on the aggregation pathway: reversible aggregates tended to have a greater proportion of hydrophobic-hydrophobic contacts and a smaller fraction of hydrophobic solvent-exposed surface area. Furthermore, the arrangement of hydrophobic patches on the protein surface played a major role in the distribution of protein contacts and solvent content. This was readily reflected in the order of the aggregates: the greater the contiguity of the hydrophobic patches on the monomer surface, the less ordered the aggregates became, despite the opportunities for rearrangement offered by a reversible pathway. These simulations have enhanced our understanding of the impact of protein structural motifs on aggregate properties and on the demarcation between aggregation and crystallization.
Related Links	http://dx.doi.org/10.1016/s0006-3495(96)79859-4
Ending Page	2902
Page Count	15
Starting Page	2888
File Format	PDF
ISSN	00063495
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	6
Volume Number	70
Language	English
Publisher Date	1996-06-01
Access Restriction	Open
Subject Keyword	Biophysics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Simulations of kinetically irreversible protein aggregate structure.

Electrophoresis in Protein Crystal: Nonequilibrium Molecular Dynamics Simulations

Structure of the stacked disk aggregate of tobacco mosaic virus protein.

Computer Simulations of Membrane Protein Folding: Structure and Dynamics

Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction

Protein conformational dynamics of crambin in crystal, solution and in the trajectories of molecular dynamics simulations

Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations

Sedimentation Patterns of Rapidly Reversible Protein Interactions

The Refined Crystal Structure of an Eel Pout Type III Antifreeze Protein RD1 at 0.62-Å Resolution Reveals Structural Microheterogeneity of Protein and Solvation

Simulations of reversible protein aggregate and crystal structure.

Similar Documents

Simulations of kinetically irreversible protein aggregate structure.

Electrophoresis in Protein Crystal: Nonequilibrium Molecular Dynamics Simulations

Structure of the stacked disk aggregate of tobacco mosaic virus protein.

Computer Simulations of Membrane Protein Folding: Structure and Dynamics

Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction

Protein conformational dynamics of crambin in crystal, solution and in the trajectories of molecular dynamics simulations

Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations

Sedimentation Patterns of Rapidly Reversible Protein Interactions

The Refined Crystal Structure of an Eel Pout Type III Antifreeze Protein RD1 at 0.62-Å Resolution Reveals Structural Microheterogeneity of Protein and Solvation

Simulations of reversible protein aggregate and crystal structure.