Literature DB >> 17433843

Protein aggregation in silico.

Troy Cellmer1, Dusan Bratko, John M Prausnitz, Harvey W Blanch.   

Abstract

Protein aggregation is a challenge to the successful manufacture of protein therapeutics; it can impose severe limitations on purification yields and compromise formulation stability. Advances in computer power, and the wealth of computational studies pertaining to protein folding, have facilitated the development of molecular simulation as a tool to investigate protein misfolding and aggregation. Here, we highlight the successes of protein aggregation studies carried out in silico, with a particular emphasis on studies related to biotechnology. To conclude, we discuss future prospects for the field, and identify several biotechnology-related problems that would benefit from molecular simulation.

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Year:  2007        PMID: 17433843      PMCID: PMC2680282          DOI: 10.1016/j.tibtech.2007.03.011

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN: 0167-7799            Impact factor:   19.536


  63 in total

1.  Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues.

Authors:  R Schwartz; S Istrail; J King
Journal:  Protein Sci       Date:  2001-05       Impact factor: 6.725

2.  Effect of rate of chemical or thermal renaturation on refolding and aggregation of a simple lattice protein.

Authors:  Hung D Nguyen; Carol K Hall
Journal:  Biotechnol Bioeng       Date:  2002-12-30       Impact factor: 4.530

3.  The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis.

Authors:  Sagar D Khare; Michael Caplow; Nikolay V Dokholyan
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-08       Impact factor: 11.205

4.  Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides.

Authors:  Hung D Nguyen; Carol K Hall
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-08       Impact factor: 11.205

5.  Influence of denatured and intermediate states of folding on protein aggregation.

Authors:  Nicolas L Fawzi; Victor Chubukov; Louis A Clark; Scott Brown; Teresa Head-Gordon
Journal:  Protein Sci       Date:  2005-04       Impact factor: 6.725

6.  Rational design of aggregation-resistant bioactive peptides: reengineering human calcitonin.

Authors:  Susan B Fowler; Stephen Poon; Roman Muff; Fabrizio Chiti; Christopher M Dobson; Jesús Zurdo
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-08       Impact factor: 11.205

Review 7.  Studies of folding and misfolding using simplified models.

Authors:  Nikolay V Dokholyan
Journal:  Curr Opin Struct Biol       Date:  2006-01-18       Impact factor: 6.809

8.  Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations.

Authors:  Hung D Nguyen; Carol K Hall
Journal:  J Am Chem Soc       Date:  2006-02-15       Impact factor: 15.419

Review 9.  Protein aggregation: folding aggregates, inclusion bodies and amyloid.

Authors:  A L Fink
Journal:  Fold Des       Date:  1998

10.  Structure of the 21-30 fragment of amyloid beta-protein.

Authors:  Andrij Baumketner; Summer L Bernstein; Thomas Wyttenbach; Noel D Lazo; David B Teplow; Michael T Bowers; Joan-Emma Shea
Journal:  Protein Sci       Date:  2006-06       Impact factor: 6.725

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  10 in total

1.  Potential aggregation-prone regions in complementarity-determining regions of antibodies and their contribution towards antigen recognition: a computational analysis.

Authors:  Xiaoling Wang; Satish K Singh; Sandeep Kumar
Journal:  Pharm Res       Date:  2010-04-27       Impact factor: 4.200

2.  Design of therapeutic proteins with enhanced stability.

Authors:  Naresh Chennamsetty; Vladimir Voynov; Veysel Kayser; Bernhard Helk; Bernhardt L Trout
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-01       Impact factor: 11.205

Review 3.  Probing protein aggregation using discrete molecular dynamics.

Authors:  Shantanu Sharma; Feng Ding; Nikolay V Dokholyan
Journal:  Front Biosci       Date:  2008-05-01

4.  Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases.

Authors:  Angel L Pey; Francois Stricher; Luis Serrano; Aurora Martinez
Journal:  Am J Hum Genet       Date:  2007-10-02       Impact factor: 11.025

5.  Extending the PRIME model for protein aggregation to all 20 amino acids.

Authors:  Mookyung Cheon; Iksoo Chang; Carol K Hall
Journal:  Proteins       Date:  2010-11-01

6.  The feeding tube of cyst nematodes: characterisation of protein exclusion.

Authors:  Sebastian Eves-van den Akker; Catherine J Lilley; James R Ault; Alison E Ashcroft; John T Jones; Peter E Urwin
Journal:  PLoS One       Date:  2014-01-28       Impact factor: 3.240

Review 7.  Food Processing: The Influence of the Maillard Reaction on Immunogenicity and Allergenicity of Food Proteins.

Authors:  Malgorzata Teodorowicz; Joost van Neerven; Huub Savelkoul
Journal:  Nutrients       Date:  2017-08-04       Impact factor: 5.717

8.  Protein Unfolding and Aggregation near a Hydrophobic Interface.

Authors:  David March; Valentino Bianco; Giancarlo Franzese
Journal:  Polymers (Basel)       Date:  2021-01-03       Impact factor: 4.329

Review 9.  Immunogenicity of therapeutic proteins: influence of aggregation.

Authors:  Kirsty D Ratanji; Jeremy P Derrick; Rebecca J Dearman; Ian Kimber
Journal:  J Immunotoxicol       Date:  2013-08-06       Impact factor: 3.000

10.  An accelerated surface-mediated stress assay of antibody instability for developability studies.

Authors:  Marie R G Kopp; Adriana-Michelle Wolf Pérez; Marta Virginia Zucca; Umberto Capasso Palmiero; Brigitte Friedrichsen; Nikolai Lorenzen; Paolo Arosio
Journal:  MAbs       Date:  2020 Jan-Dec       Impact factor: 5.857

  10 in total

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