The State of Proteins not with Standing, Translational Velocity is Vital for their Function

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Ikechukwu Iloh Udema
Abraham Olalere Onigbinde


Background: Targeting of macromolecules by means of translational diffusion for therapeutic reason is generally of interest. But translational velocity that enables directional delivery of any molecule on target is given less attention.

Objectives: The objectives of this research are to: 1) determine the value of the cohesion factor affecting solutes, 2) determine the translational velocity of porcine pancreatic (PPAA) - and human salivary (HSAA) – alpha amylase and ions, 3) rederive the effective kinetic energy (K.E.) of solutes, 4) determine the thermodynamic parameters for a folded to an unfolded transition and 5) give reasons why the velocity of solution components is generally very important.

Methods: A theoretical research and experimentation using Bernfeld method.

Results and Discussion: The K.E. of solution components as re-derived is « 3kBT / 2 (where kB and T are Boltzmann constant and Kelvin temperature respectively.). The velocities of hydrolysis of the substrate with the sucrose-treated PPAA were generally higher than those of HSAA. The values of conformational entropy change (∆Sconf) for PPAA were generally higher than those of HSAA. Expectedly the values of ∆Sconf were positive.

Conclusion: In conclusion, the square root of the cohesion factor is larger than 22.4 exp (+3) 310.15 K / 273.15 K / 18, accounting for the translational velocity (u) in solution being « gas phase velocity (U). The translational diffusion D and u remain respectively, a function of the hydrodynamic radius of the solutes in particular and the magnitude of D; unfolding of proteins decreases the values of the parameters. Overall, unfolding is entropy driven. Without the mobility of solution components at desired velocity directional delivery of small molecules to site of need such as intrinsically disordered proteins etc may remain impossible.

Alpha amylases, thermodynamic parameters, cohesion factor, translational velocity, diffusion coefficient, effective kinetic energy, unfolded, intrinsically disordered proteins

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How to Cite
Udema, I., & Onigbinde, A. (2019). The State of Proteins not with Standing, Translational Velocity is Vital for their Function. Asian Journal of Research in Biochemistry, 5(3), 1-17.
Original Research Article


Loman A, Gregor I, Stutz C, Mund M, Enderlein J. Measuring rotational diffusion of macromolecules by fluorescence correlation spectroscopy. Photochem. Photobiol. Sci. 2010;9:627–636.

Lee KG The effect of slow substrate diffusion on the activity, stability, and selectivity of immobilized enzymes: A theoretical and experimental study. Thesis Iowa State University; 1978.

Długosz M, Trylska J. Diffusion in crowded biological environments: Applications of Brownian dynamics. Biophysics. 2011;4(3): 1-12.

Bhakuni V. Alcohol-induced molten globule intermediates of proteins: Are they real folding intermediates or off pathway products? Arch. Biochem. Biophys. 1998; 357(2):274-284.

Kamei T, Oobatake M, Suzuki M. Hydration of apomyoglobin in native, molten globule and unfolded states by using microwave dielectric spectroscopy. Biophys. J. 2002;418-425.

Koshiba T, Kobasigawa Y. Energetics of three-state unfolding of a protein: Canine milk lysozyme. Protein Eng. 2001;14(12): 967-974.

Zeleznak KJ, Hoseney RC. The glass transition in starch. Cereal Chem. 1987;64 (2):121-124.

Van Oijen AM. Cutting the forest to see a single? Nat Chem. Biol. 2008;4(8):440-443.

Stefani M. Protein misfolding and aggregation: New examples in medicine and biology of the dark side of the protein world Biochimica et Biophysica Acta. 2004; 1739:5–25.

Kelly J. Alternative conformation of amyloidogenic proteins and their multi-step assembly pathways. Curr. Opin. Struck. Biol. 1998;8:101–106.

Dobson CM. The structural basis of protein folding and its links with human disease, Philos. Trans. R. Soc. Lond. B. 2001;356: 133–145.

Reilly MM. Genetically determined neuropathies, J. Neurol. 1998;245:6–13.

Uversky VN. Intrinsically disordered proteins from A to Z. Int J Biochem Cell Biol. 2011;43:1090–1103.

Tompa P. Unstructural biology coming of age. Curr Med Res Opin. 2011;21:419–425.

Iakoucheva LM, Brown CJ, Lawson JD, Obradovic Z, Dunker AK. Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol. 2002;323:573–584.

Udema II. In vitro investigation into the effects of ethanol, aspirin, and stabilisers on mesophilic alpha amylases. Thesis. AAU Ekpoma; 2013.

Udema II. Determination of translational velocity of reaction mixture components: Effect on the rate of reaction. Adv. Biochem. 2016;4(6):84-93.

Šoltésová M, Benda L, Peksa M, Czernek J, Lang J. Determination of size ofmolecular clusters of ethanol by means of NMR diffusometry and hydrodynamic calculations. J. Phys. Chem. B. 2014;118: 6864-6874.

Moyer LS, Abramson HA. Electrokinetic aspects of surface chemistry V. Electric mobility and titration curves of proteins and their relationship to the calculation of radius and molecular weight. J. Biol. Chem. 1938;123:391-403.

Fitter J. A measure of conformational entropy change during thermal protein unfolding using neutron spectroscopy. Biophys. J. 2003;84:3924-3930.

Udema II, Onigbinde AO. Theoretical investigation into the change in the number of water molecules in solvent inaccessible region of an enzyme and enzyme-substrate complex. Asian J. Res. Biochem. 2019;5(2):1-17.

Baskakov I, Bolen DW. Forcing thermodynamically unfolded proteins to fold (communication). J. Biol. Chem. 1998; 273(9):1-5.

Effect of interacting organic co-solutes with enzyme substrate complex on the hydrolysis of raw soluble starch with alpha-amylase: Theory and experimentation Adv. Res. 2016;7(1):1-19.

Bernfeld P. Amylases, alpha and beta. Methods. Enzymol. 1955;1:149–152.

Hozo SP, Djulbegovic B, Hozo I. Estimating the means and variance from the median range and the size of a sample. BMC Med. Res. Methodol. 2005; 5(13):1-10.

Klabunde T, Petrassi HM, Oza VB, Raman P, Kelly JW, et al. Rational design of potent human transthyretin amyloid disease inhibitors. Nat. Struct. Biol. 2000; 7:312–321.

Bulawa CE, Connelly S, Devit M, Wang L, Weigel C, et al. Tafamidis, a potent and selective transthyretin kinetic stabilizer that inhibits the amyloid cascade. Proc. Nat. Acad. Sci. USA. 2012;109:9629–9634.

Orwig SD, Tan YL, Grimster NP, Yu Z, Powers ET, et al. Binding of 3,4,5,6-tetrahydroxyazepanes to the acid-beta-glucosidase active site: Implications for pharmacological chaperone design for Gaucher disease. Biochemistry. 2011;50: 10647–10657.

Tóth G, Gardai SJ, Zago W, Bertoncini CW, Cremades N, et al. Targeting the intrinsically disordered structural ensemble of a-synuclein by small molecules as a potential therapeutic strategy for Parkinson’s disease. PLOS ONE. 2014;9 (2):1-12.

Michel J, Cuchillo R. The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-Myc. PLoS ONE. 2010;7(7): e41070. 1-13.

Schurr JM. The role of diffusion in enzyme kinetic. Biophys. J. 1970;10:717-727.

Pollard EC. The control of cell growth. In Cell Biology in Medicine (Bittar EE. ed). New York, London, Sydney, Toronto: John Wiley & Sons, Inc. 1973;367.

Tzafriri AR, Garcia-Polite F, Li X, Keating J, Balaguer JM, et al. Defining drug and target protein distributions after stent-based drug release: durable versus deployable coatings. J. Control Release. 2018;28(274):102–108.

Pollard EC. Physical aspects of protein and DNA synthesis J. Theor. Biol. 1961;1 (3):328-341.

Pollard EC. Collision kinetics applied to phage synthesis, messenger RNA, and glucose metabolism. J. Theor. Biol. 1963; 4(1):98-112.

Heller GT, Sormanni P, Vendruscolo M. Targeting disordered proteins with small molecules using entropy. Trends Biochem Sci. 2015;40(9):491-496.

Timasheff SN. Protein solvent preferential interaction, protein hydration, and the modulation of biochemical reactions by solvent components. Biochemistry. 2002; 99(15):9721-9726.

Rösgen J, Pettit MB, Bolen DW. Structure of solutions of aqueous biochemical compounds-pair correlations. Biophys. J. 2005;89:2988–2997.

D’ Amico S, Marx JC, Gerday C, Feller G. Activity – Stability relationships in extremophilic enzymes. J. Biol. Chem. 2003;276(10):7891-7896.

Cipolla A, Delbrassine F, Da Lage JL, Feller G. Temperature adaptations in psychrophilic, mesophilic and thermophilic chloride-dependent alpha-amylases. Biochemie. 2012;94(9):1943-1950.

Nonell-Canals A, Sanchez-Martinez M. Intrinsically disordered proteins as drug targets. MOJ Proteomics Bioinform. 2017; 5(2):69‒73.

Heller GT, Bonomi M, Vendruscolo M. Structural ensemble modulation upon small-molecule binding to disordered proteins. J. Mol. Biol. 2018;430(16):2288-2292.

Kendrick BS, Chang BS, Arakawa T, Peterson B, Randalph TW, Manning MC, et al Preferential exclusion of sucrose from recombinant interleukin-1 receptor antagonist: Role in restricted conformational mobility and compaction of native state. Proc. Nat. Acad. Sci. U.S.A. 1997;94:11917-11920.

Alsaggar M, Liu D. Organ-based drug delivery J. Drug. Targeting. 2018;26(5-6): 385-397.

Allec N, Choi M, Yesupriya N, Szychowski B, White MR, Kann MG, et al. Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept. Sci. Rep. 2015;5(12085):1-12.

Kirkwood JG, Buff FP. The statistical mechanical theory of solutions. J. Chem. Phys. 1951;19:774–777.

Hastings CL, Roche ET, Ruiz-Hernandez E, Schenke-Layland K, Walsh CJ, Duffy GP. Drug and cell delivery for cardiac regeneration. Adv. Drug Deliv. Rev. 2015; 84:85-106.

Bhise NS, Ribas J, Manoharan V, Zhang YS, Polini A, Massa S, et al. Organ-on-a-Chip platforms for studying drug delivery systems. J. Control Release. 2014;190: 82-93.

Bode C, Bode CJ. Alcohol’s role in gastrointestinal tract disorders. Alcohol Health and Res. World. 1997;21(1):76-83.

Lieber CS. Alcohol and its role in hepatic and extra-hepatic diseases. Mt Sinai J. Med. 2000;67(1):84-90.

Huang CC, Chen JR, Liu CC, Chen KT, Shieh MJ, Yang SC. Effects of long-term ethanol consumption on jejunal lipase and disaccharides activities in male and female rats. World J. Gastroenterol. 2005;11(17): 2603-2608.

Halsted CH, Robles EA, Mezey E. Distribution of ethanol in the human gastro intestinal tract American J. Clin. Nutr. 1973;26:831-834.