title: Role of single-point mutations and deletions on transition temperatures in ideal proteinogenic heteropolymer chains in the gas phase.
abstract: A coarse-grained statistical mechanics-based model for ideal heteropolymer proteinogenic chains of non-interacting residues is presented in terms of the size K of the chain and the set of helical propensities [Formula: see text] associated with each residue j along the chain. For this model, we provide an algorithm to compute the degeneracy tensor [Formula: see text] associated with energy level [Formula: see text] where [Formula: see text] is the number of residues with a native contact in a given conformation. From these results, we calculate the equilibrium partition function [Formula: see text] and characteristic temperature [Formula: see text] at which a transition from a low to a high entropy states is observed. The formalism is applied to analyze the effect on characteristic temperatures [Formula: see text] of single-point mutations and deletions of specific amino acids [Formula: see text] along the chain. Two probe systems are considered. First, we address the case of a random heteropolymer of size K and given helical propensities [Formula: see text] on a conformational phase space. Second, we focus our attention to a particular set of neuropentapeptides, [Met-5] and [Leu-5] enkephalins whose thermodynamic stability is a key feature on their coupling to [Formula: see text] and [Formula: see text] receptors and the triggering of biochemical responses.
authors.affiliation: Colegio de Ciencia y Tecnologia and Posgrado en Ciencias de la Complejidad, Universidad Autonoma de la Ciudad de Mexico, Prol Av San Isidro 151, Deleg Iztapalapa, CP 09760, Mexico, DF, Mexico. luis.olivares@uacm.edu.mx.
authors.forename: L
authors.initials: L
authors.lastname: Olivares-Quiroz
mesh_terms: D005740:Gases / Q000737:chemistry*; D008958:Models, Molecular; D017354:Point Mutation; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D017384:Sequence Deletion; D044366:Transition Temperature
chemical_list: D005740:Gases; D011506:Proteins
keywords: Canonical ensemble; Conformational phase transitions; Equilibrium statistical mechanics; Ideal heteropolymers; Random heteropolymers; Single-point mutations; Specific heat proteins
references.citation: Phys Rev Lett. 2011 Mar 18;106(11):118102
references.pmid: 21469900
references.citation: Annu Rev Biophys. 2008;37:289-316
references.pmid: 18573083
references.citation: Int J Mol Sci. 2015 Mar 06;16(3):5194-215
references.pmid: 25756377
references.citation: Protein Eng Des Sel. 2011 Jan;24(1-2):11-9
references.pmid: 21051320
references.citation: Macromol Biosci. 2011 Jan 10;11(1):50-9
references.pmid: 21136535
references.citation: Chemphyschem. 2008 May 16;9(7):954-66
references.pmid: 18348129
references.citation: World J Gastroenterol. 2014 Mar 7;20(9):2218-23
references.pmid: 24605021
references.citation: Invest New Drugs. 2013 Aug;31(4):1066-70
references.pmid: 23275062
references.citation: J Phys Condens Matter. 2013 Apr 17;25(15):155103
references.pmid: 23515207
references.citation: Proc Natl Acad Sci U S A. 1995 Oct 10;92(21):9801-4
references.pmid: 7568221
references.citation: Protein Sci. 1994 May;3(5):843-52
references.pmid: 8061613
references.citation: Regul Toxicol Pharmacol. 2011 Apr;59(3):385-90
references.pmid: 21215785
references.citation: J Mol Graph Model. 2001;19(1):102-18
references.pmid: 11381520
references.citation: Cancer Lett. 2014 Mar 28;344(2):212-22
references.pmid: 24291668
references.citation: Mass Spectrom Rev. 2001 Nov-Dec;20(6):402-22
references.pmid: 11997946
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D1063-9
references.pmid: 24137000
references.citation: Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10652-6
references.pmid: 9380690
references.citation: J Phys Chem B. 2009 Jul 2;113(26):8800-12
references.pmid: 19453123
references.citation: Peptides. 2013 Dec;50:55-95
references.pmid: 24126281
references.citation: Nat Cell Biol. 2013 Jan;15(1):2-8
references.pmid: 23263379
references.citation: Am J Gastroenterol Suppl. 2014 Sep 10;2(1):17-21
references.pmid: 25207608
references.citation: Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5937-41
references.pmid: 1631077
references.citation: Protein Sci. 1995 Jul;4(7):1325-36
references.pmid: 7670375
references.citation: Biophys J. 2006 Oct 1;91(7):2399-404
references.pmid: 16829555
references.citation: Hum Mutat. 2005 Nov;26(5):399-412
references.pmid: 16138310
references.citation: Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):20-2
references.pmid: 1729690
references.citation: Brain Res Brain Res Rev. 2002 Feb;38(3):351-76
references.pmid: 11890982
references.citation: Biopolymers. 1991 Nov;31(13):1463-70
references.pmid: 1814498
references.citation: J Am Chem Soc. 2013 Jan 30;135(4):1177-80
references.pmid: 23320566
references.citation: J Mol Biol. 1998 Apr 24;278(1):279-89
references.pmid: 9571050
references.citation: Philos Trans A Math Phys Eng Sci. 2005 Feb 15;363(1827):453-64; discussion 464-7
references.pmid: 15664893
references.citation: Life Sci. 1988;43(16):1313-8
references.pmid: 2845218
references.citation: Proc Natl Acad Sci U S A. 1987 Oct;84(19):6611-5
references.pmid: 3477791