Literature DB >> 23754389

Stabilization of a protein conferred by an increase in folded state entropy.

Shlomi Dagan1, Tzachi Hagai, Yulian Gavrilov, Ruti Kapon, Yaakov Levy, Ziv Reich.   

Abstract

Entropic stabilization of native protein structures typically relies on strategies that serve to decrease the entropy of the unfolded state. Here we report, using a combination of experimental and computational approaches, on enhanced thermodynamic stability conferred by an increase in the configurational entropy of the folded state. The enhanced stability is observed upon modifications of a loop region in the enzyme acylphosphatase and is achieved despite significant enthalpy losses. The modifications that lead to increased stability, as well as those that result in destabilization, however, strongly compromise enzymatic activity, rationalizing the preservation of the native loop structure even though it does not provide the protein with maximal stability or kinetic foldability.

Keywords:  loop closure entropy; molecular dynamics; protein folding

Mesh:

Substances:

Year:  2013        PMID: 23754389      PMCID: PMC3696814          DOI: 10.1073/pnas.1302284110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  39 in total

1.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

Authors:  C Clementi; H Nymeyer; J N Onuchic
Journal:  J Mol Biol       Date:  2000-05-19       Impact factor: 5.469

2.  Three key residues form a critical contact network in a protein folding transition state.

Authors:  M Vendruscolo; E Paci; C M Dobson; M Karplus
Journal:  Nature       Date:  2001-02-01       Impact factor: 49.962

3.  Determination of a transition state at atomic resolution from protein engineering data.

Authors:  Emanuelel Paci; Michele Vendruscolo; Christopher M Dobson; Martin Karplus
Journal:  J Mol Biol       Date:  2002-11-15       Impact factor: 5.469

4.  Low free energy cost of very long loop insertions in proteins.

Authors:  Michelle Scalley-Kim; Philippe Minard; David Baker
Journal:  Protein Sci       Date:  2003-02       Impact factor: 6.725

5.  Three-dimensional structure of acylphosphatase. Refinement and structure analysis.

Authors:  A Pastore; V Saudek; G Ramponi; R J Williams
Journal:  J Mol Biol       Date:  1992-03-20       Impact factor: 5.469

Review 6.  Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins.

Authors:  Huan-Xiang Zhou
Journal:  Acc Chem Res       Date:  2004-02       Impact factor: 22.384

7.  Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding.

Authors:  J K Myers; C N Pace; J M Scholtz
Journal:  Protein Sci       Date:  1995-10       Impact factor: 6.725

8.  Arginine-23 is involved in the catalytic site of muscle acylphosphatase.

Authors:  N Taddei; M Stefani; M Vecchi; A Modesti; G Raugei; M Bucciantini; F Magherini; G Ramponi
Journal:  Biochim Biophys Acta       Date:  1994-09-21

9.  Looking for residues involved in the muscle acylphosphatase catalytic mechanism and structural stabilization: role of Asn41, Thr42, and Thr46.

Authors:  N Taddei; M Stefani; F Magherini; F Chiti; A Modesti; G Raugei; G Ramponi
Journal:  Biochemistry       Date:  1996-06-04       Impact factor: 3.162

10.  Equilibrium unfolding studies of horse muscle acylphosphatase.

Authors:  N Taddei; M Buck; R W Broadhurst; M Stefani; G Ramponi; C M Dobson
Journal:  Eur J Biochem       Date:  1994-11-01
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  15 in total

1.  Nonspecific yet decisive: Ubiquitination can affect the native-state dynamics of the modified protein.

Authors:  Yulian Gavrilov; Tzachi Hagai; Yaakov Levy
Journal:  Protein Sci       Date:  2015-06-09       Impact factor: 6.725

2.  Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Gō model.

Authors:  Ji-Guo Su; Xiao-Ming Han; Shu-Xin Zhao; Yan-Xue Hou; Xing-Yuan Li; Li-Sheng Qi; Ji-Hua Wang
Journal:  J Mol Model       Date:  2016-03-28       Impact factor: 1.810

3.  Natural and Synthetic Suppressor Mutations Defy Stability-Activity Tradeoffs.

Authors:  Sonya Lee; Cynthia N Okoye; Devin Biesbrock; Emily C Harris; Katelyn F Miyasaki; Ryan G Rilinger; Megalan Tso; Kathryn M Hart
Journal:  Biochemistry       Date:  2022-02-10       Impact factor: 3.162

4.  Deletion of the Loop Linking Two Domains of Exo-Inulinase InuAMN8 Diminished the Enzymatic Thermo-Halo-Alcohol Tolerance.

Authors:  Xiaolong Cen; Rui Zhang; Limei He; Xianghua Tang; Qian Wu; Junpei Zhou; Zunxi Huang
Journal:  Front Microbiol       Date:  2022-06-23       Impact factor: 6.064

Review 5.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Authors:  Fabio Sterpone; Simone Melchionna; Pierre Tuffery; Samuela Pasquali; Normand Mousseau; Tristan Cragnolini; Yassmine Chebaro; Jean-Francois St-Pierre; Maria Kalimeri; Alessandro Barducci; Yoann Laurin; Alex Tek; Marc Baaden; Phuong Hoang Nguyen; Philippe Derreumaux
Journal:  Chem Soc Rev       Date:  2014-04-23       Impact factor: 54.564

6.  Mechanistic basis for ubiquitin modulation of a protein energy landscape.

Authors:  Emma C Carroll; Naomi R Latorraca; Johanna M Lindner; Brendan C Maguire; Jeffrey G Pelton; Susan Marqusee
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-23       Impact factor: 12.779

7.  Protein folding as a complex reaction: a two-component potential for the driving force of folding and its variation with folding scenario.

Authors:  Sergei F Chekmarev
Journal:  PLoS One       Date:  2015-04-07       Impact factor: 3.240

8.  Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome.

Authors:  Yun-Tzai Cloud Lee; Chia-Yun Chang; Szu-Yu Chen; Yun-Ru Pan; Meng-Ru Ho; Shang-Te Danny Hsu
Journal:  Sci Rep       Date:  2017-03-24       Impact factor: 4.379

9.  Site-specific amino acid substitution in dodecameric peptides determines the stability and unfolding of c-MYC quadruplex promoting apoptosis in cancer cells.

Authors:  Pallabi Sengupta; Nilanjan Banerjee; Tanaya Roychowdhury; Anindya Dutta; Samit Chattopadhyay; Subhrangsu Chatterjee
Journal:  Nucleic Acids Res       Date:  2018-11-02       Impact factor: 16.971

10.  Exploring conformational preferences of proteins: ionic liquid effects on the energy landscape of avidin.

Authors:  Talia A Shmool; Laura K Martin; Coby J Clarke; Liem Bui-Le; Karen M Polizzi; Jason P Hallett
Journal:  Chem Sci       Date:  2020-10-23       Impact factor: 9.825

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