BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2022 Dec 11

PMID 36499696

Authors

Mina Nikolic

Sandi Brudar

Evangelos Coutsias

Ken A Dill

Miha Luksic

Carlos Simmerling

Barbara Hribar-Lee

Affiliations

Soon will be listed here.

Abstract

We present here a freely available web-based database, called BioMThermDB 1.0, of thermophysical and dynamic properties of various proteins and their aqueous solutions. It contains the hydrodynamic radius, electrophoretic mobility, zeta potential, self-diffusion coefficient, solution viscosity, and cloud-point temperature, as well as the conditions for those determinations and details of the experimental method. It can facilitate the meta-analysis and visualization of data, can enable comparisons, and may be useful for comparing theoretical model predictions with experiments.

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References

Wang W . Protein aggregation and its inhibition in biopharmaceutics. Int J Pharm. 2005; 289(1-2):1-30. DOI: 10.1016/j.ijpharm.2004.11.014. View

Kumar M, Gromiha M . PINT: Protein-protein Interactions Thermodynamic Database. Nucleic Acids Res. 2005; 34(Database issue):D195-8. PMC: 1347380. DOI: 10.1093/nar/gkj017. View

Yadav S, Scherer T, Shire S, Kalonia D . Use of dynamic light scattering to determine second virial coefficient in a semidilute concentration regime. Anal Biochem. 2010; 411(2):292-6. DOI: 10.1016/j.ab.2010.12.014. View

Jaklin M, Hritz J, Hribar-Lee B . A new fibrillization mechanism of β-lactoglobulin in glycine solutions. Int J Biol Macromol. 2022; 216:414-425. PMC: 10039397. DOI: 10.1016/j.ijbiomac.2022.06.182. View

Brudar S, Hribar-Lee B . Effect of Buffer on Protein Stability in Aqueous Solutions: A Simple Protein Aggregation Model. J Phys Chem B. 2021; 125(10):2504-2512. PMC: 8041305. DOI: 10.1021/acs.jpcb.0c10339. View

Kastelic M, Dill K, Kalyuzhnyi Y, Vlachy V . Controlling the viscosities of antibody solutions through control of their binding sites. J Mol Liq. 2019; 270:234-242. PMC: 6425977. DOI: 10.1016/j.molliq.2017.11.106. View

Kulandaisamy A, Sakthivel R, Gromiha M . MPTherm: database for membrane protein thermodynamics for understanding folding and stability. Brief Bioinform. 2020; 22(2):2119-2125. DOI: 10.1093/bib/bbaa064. View

Brudar S, Hribar-Lee B . The Role of Buffers in Wild-Type HEWL Amyloid Fibril Formation Mechanism. Biomolecules. 2019; 9(2). PMC: 6406783. DOI: 10.3390/biom9020065. View

Kastelic M, Kalyuzhnyi Y, Hribar-Lee B, Dill K, Vlachy V . Protein aggregation in salt solutions. Proc Natl Acad Sci U S A. 2015; 112(21):6766-70. PMC: 4450416. DOI: 10.1073/pnas.1507303112. View

10.

Mason B, Zhang-Van Enk J, Zhang L, Remmele Jr R, Zhang J . Liquid-liquid phase separation of a monoclonal antibody and nonmonotonic influence of Hofmeister anions. Biophys J. 2010; 99(11):3792-800. PMC: 2998619. DOI: 10.1016/j.bpj.2010.10.040. View

11.

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

12.

Zidar M, Rozman P, Belko-Parkel K, Ravnik M . Control of viscosity in biopharmaceutical protein formulations. J Colloid Interface Sci. 2020; 580:308-317. DOI: 10.1016/j.jcis.2020.06.105. View

13.

Nikam R, Kulandaisamy A, Harini K, Sharma D, Gromiha M . ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years. Nucleic Acids Res. 2020; 49(D1):D420-D424. PMC: 7778892. DOI: 10.1093/nar/gkaa1035. View

14.

Jemimah S, Yugandhar K, Gromiha M . PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics. Bioinformatics. 2017; 33(17):2787-2788. DOI: 10.1093/bioinformatics/btx312. View