Revisiting "reverse hydrophobic effect": applicable only to coil mutations at the surface.

Abstract:

:In a seminal paper, Pakula and Sauer (Nature, 1990, 344, 363-364) demonstrated that the increase in side-chain hydrophobicity has a reverse relationship with protein stability. We have addressed this problem with several examples of mutants that span at different locations in protein structure based on secondary structure and solvent accessibility. We confirmed that the stability change upon single coil mutation at exposed region is reversely correlated with hydrophobicity with a single exception. In addition, we found the existence of such relationship in partially buried coil mutants. The stability of exposed helical mutants is governed by conformational properties. In buried and partially buried helical and strand mutants properties reflecting hydrophobicity have direct relationship with stability, whereas an opposite relationship was obtained with entropy and flexibility. The structural analysis of partially buried/exposed mutants showed that the surrounding residues are important for the stability change upon mutation. These results provide insights to understand the general behavior for the stability of proteins upon amino acid substitutions.

journal_name

Biopolymers

journal_title

Biopolymers

authors

Gromiha MM

doi

10.1002/bip.21187

subject

Has Abstract

pub_date

2009-07-01 00:00:00

pages

591-9

issue

7

eissn

0006-3525

issn

1097-0282

journal_volume

91

pub_type

杂志文章
  • Optical tweezers experiments resolve distinct modes of DNA-protein binding.

    abstract::Optical tweezers are ideally suited to perform force microscopy experiments that isolate a single biomolecule, which then provides multiple binding sites for ligands. The captured complex may be subjected to a spectrum of forces, inhibiting or facilitating ligand activity. In the following experiments, we utilize opti...

    journal_title:Biopolymers

    pub_type: 杂志文章,评审

    doi:10.1002/bip.21123

    authors: McCauley MJ,Williams MC

    更新日期:2009-04-01 00:00:00

  • Extraction and characterization of a natural rubber from Euphorbia characias latex.

    abstract::A natural rubber was identified and characterized for the first time in the latex of the perennial Mediterranean shrub Euphorbia characias. Four different methods, i.e., acetone, acetic acid, trichloroacetic acid, and Triton® X-100, followed by successive treatments with cyclohexane/ethanol, were employed to extract t...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.22044

    authors: Spanò D,Pintus F,Mascia C,Scorciapino MA,Casu M,Floris G,Medda R

    更新日期:2012-08-01 00:00:00

  • Vibrations-determined properties of green fluorescent protein.

    abstract::The physicochemical characteristics of the green fluorescent protein (GFP), including the thermodynamic properties (entropy, enthalpy, Gibbs' free energy, heat capacity), normal mode vibrations, and atomic fluctuations, were investigated. The Gaussian 03 computational chemistry program was employed for normal mode ana...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.20264

    authors: Krasnenko V,Tkaczyk AH,Tkaczyk ER,Farkas O,Mauring K

    更新日期:2005-06-15 00:00:00

  • Self-aggregation properties of spin-labeled zervamicin IIA as studied by PELDOR spectroscopy.

    abstract::In this article, the pulsed double electron-electron resonance in electron spin-echo (PELDOR) technique is applied to study the self-aggregation of spin-labeled zervamicin IIA, a hexadecapeptide antibiotic of fungal origin, which is known to form ion channels in a phospholipid double layer. Measurements of the ion cha...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.10208

    authors: Milov AD,Tsvetkov YD,Gorbunova EY,Mustaeva LG,Ovchinnikova TV,Raap J

    更新日期:2002-09-01 00:00:00

  • The use of spectral decomposition via the convex constraint algorithm in interpreting the CD-observed unfolding transitions of coiled coils.

    abstract::Decomposition of CD spectra for the unfolding of both coiled-coil and single-helical molecules is carried out via the convex constraint algorithm (CCA) [A. Perczel, M. Hollósi, G. Tusnády, and G. D. Fasman (1991) Protein Engineering, Vol. 4, pp. 669-679]. Examined are (1) our thermal unfolding data for rabbit alpha al...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.360360310

    authors: Holtzer ME,Holtzer A

    更新日期:1995-09-01 00:00:00

  • Long-range structural effects in supercoiled DNA: statistical thermodynamics reveals a correlation between calculated cooperative melting and contextual influence on cruciform extrusion.

    abstract::We have previously described [K. M. Sullivan and D. M. J. Lilley (1986) Cell 47, 817-827] a set of sequences, called C-type inducing sequences, which cause cruciform extrusion by adjacent inverted repeats to occur by an abnormal kinetic pathway involving a large denatured region of DNA. In this paper we apply statisti...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.360280810

    authors: Schaeffer F,Yeramian E,Lilley DM

    更新日期:1989-08-01 00:00:00

  • Does the anesthetic 2,2,2-trifluoroethanol interact with bovine serum albumin by direct binding or by solvent-mediated effects? A calorimetric and spectroscopic investigation.

    abstract::Thermal unfolding of bovine serum albumin (BSA) has been studied in the presence of 2,2,2-trifluoroethanol (TFE) using high-sensitivity microdifferential scanning calorimetry. Quantitative thermodynamic parameters accompanying the thermal transitions have been evaluated. TFE is observed to be a stabilizer or a destabi...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.20262

    authors: Banerjee T,Kishore N

    更新日期:2005-06-05 00:00:00

  • Formation of structured polymers upon controlled denaturation of beta-lactoglobulin with different chaotropes.

    abstract::Prolonged exposure (>90 days) of bovine beta-lactoglobulin (BLG) to subdenaturing concentrations of either urea or potassium thiocyanate resulted in the formation of ordered polymers in the form of fibrils. The fibrils obtained with each chaotrope showed major differences in morphology, surface properties, thiol acces...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.20704

    authors: Rasmussen P,Barbiroli A,Bonomi F,Faoro F,Ferranti P,Iriti M,Picariello G,Iametti S

    更新日期:2007-05-01 00:00:00

  • Conformation-activity relationship of a novel peptide antibiotic: structural characterization of dermaseptin DS 01 in media that mimic the membrane environment.

    abstract::Dermaseptins, small polycationic peptides synthesized by amphibians, exert a lytic action on bacteria, protozoa, yeast, and filamentous fungi at micromolar concentrations, but unlike polylysines, show little hemolytic activity. Dermaseptins S are active only against bacteria and form aggregates at high peptide/lipid r...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.20244

    authors: Castiglione-Morelli MA,Cristinziano P,Pepe A,Temussi PA

    更新日期:2005-01-01 00:00:00

  • Morphology and aggregation of RADA-16-I peptide Studied by AFM, NMR and molecular dynamics simulations.

    abstract::RADA-16-I is a self-assembling peptide which forms biocompatible fibrils and hydrogels. We used molecular dynamics simulations, atomic-force microscopy, NMR spectroscopy, and thioflavin T binding assay to examine size, structure, and morphology of RADA-16-I aggregates. We used the native form of RADA-16-I (H-(ArgAlaAs...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.22755

    authors: Bagrov D,Gazizova Y,Podgorsky V,Udovichenko I,Danilkovich A,Prusakov K,Klinov D

    更新日期:2016-01-01 00:00:00

  • A minimalistic 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists.

    abstract::Because of its involvement in HIV entry, the chemokine receptor CXCR4 is an attractive target for antiretroviral drugs. Despite the large number of CXCR4 inhibitors studied, the 3D pharmacophore for binding to CXCR4 remains elusive, mainly as a result of conformational flexibility inherent in the identified ligands. I...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.20508

    authors: Våbenø J,Nikiforovich GV,Marshall GR

    更新日期:2006-01-01 00:00:00

  • Fourier transform infrared spectroscopy suggests unfolding of loop structures precedes complete unfolding of pig citrate synthase.

    abstract::Pig citrate synthase (PCS) can be used as a model enzyme to gain some insight into the structural basis of protein thermostability. The thermal unfolding characteristics of the specific secondary structure elements within PCS were monitored in detail by following changes in its amide I band components. The result of o...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.10392

    authors: Severcan F,Haris PI

    更新日期:2003-08-01 00:00:00

  • External reversible control of recognition behavior of alpha-peptide ribonucleic acid (alpha-PRNA) through anti-syn orientational switching of the nucleobase induced by borate esterification of the cis-2',3'-diol.

    abstract::A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5'-amino-5'-deoxypyrimidine ribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary polynucleotide through the orie...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.10563

    authors: Wada T,Sato H,Inoue Y

    更新日期:2004-01-01 00:00:00

  • Dielectric study on hydration of B-, A-, and Z-DNA.

    abstract::Dielectric relaxation peak due to bound water was found around 100 MHz in poly(dG-dC).poly(dG-dC) and calf thymus DNA in water-ethanol mixtures with NaCl buffer. Relaxation time and strength show a transition for poly(dG-dC).poly(dG-dC) at an ethanol composition Cw = 0.45 (w/w) where the structural transition from B- ...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.360300702

    authors: Umehara T,Kuwabara S,Mashimo S,Yagihara S

    更新日期:1990-01-01 00:00:00

  • Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules.

    abstract::The experimental thermodynamic data for the dissolution of five simple hydrocarbon molecules in water were combined with the solute-solvent interaction energy from a computer simulation study to yield data on the enthalpy change of solvent reorganization. Similar data were generated for dissolving these same solute mo...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.360310809

    authors: Lee B

    更新日期:1991-07-01 00:00:00

  • Individual-site binding data and the energetics of protein-DNA interactions.

    abstract::Individual-site isotherms for the binding of bacteriophage lambda repressor to the left and right lambda operators have been determined [D. F. Senear, M. Brenowitz, M. A. Shea, and G. K. Ackers (1986) Biochemistry, Vol. 25, pp. 7344-7354.] using the DNAse protection technique [footprinting; D. J. Galas and A. Schmitz ...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.360330903

    authors: Saroff HA

    更新日期:1993-09-01 00:00:00

  • Hairpin ribozyme catalysis: a surface-enhanced Raman spectroscopy study.

    abstract::The existence of an "RNA world" as an early step in the history of life increases the interest for the characterization of these biomolecules. The hairpin ribozyme studied here is a self-cleaving/ligating motif found in the minus strand of the satellite RNA associated with Tobacco ringspot virus. Surface-enhanced Rama...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.21143

    authors: Percot A,Lecomte S,Vergne J,Maurel MC

    更新日期:2009-05-01 00:00:00

  • Structural features and biological activities of the cathelicidin-derived antimicrobial peptides.

    abstract::Cathelicidins are a numerous group of mammalian proteins that carry diverse antimicrobial peptides at the C-terminus of a highly conserved preproregion. These peptides, which become active when released from the proregion, display a remarkable variety of sizes, sequences, and structures, and in fact comprise represent...

    journal_title:Biopolymers

    pub_type: 杂志文章,评审

    doi:10.1002/1097-0282(2000)55:1<31::AID-BIP40>3.0.CO;2

    authors: Gennaro R,Zanetti M

    更新日期:2000-01-01 00:00:00

  • Prediction of the binding mode between GSK3β and a peptide derived from GSKIP using molecular dynamics simulation.

    abstract::GSK3β plays an important role in many physiological functions; dysregulated GSK3β is involved in human diseases such as diabetes, cancer, and Alzheimer's disease. This study uses MD simulations to determine the interaction between GSK3β and a peptide derived from GSKIP, a novel GSK3β interacting protein. Results show ...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.21603

    authors: Tang XN,Lo CW,Chuang YC,Chen CT,Sun YC,Hong YR,Yang CN

    更新日期:2011-07-01 00:00:00

  • Site-selective modification of peptides: From "customizable units" to novel α-aryl and α-alkyl glycine derivatives, and components of branched peptides.

    abstract::The creation of peptide libraries by site-selective modification of a few peptide substrates would increase the efficiency of discovery processes, but still is a real synthetic challenge. The site-selective modification of small peptides at serine or threonine residues, by using a short scission-addition procedure, al...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.22642

    authors: Romero-Estudillo I,Saavedra C,Boto A,Álvarez E

    更新日期:2015-09-01 00:00:00

  • Possible formation of the left-handed α-helix of poly-L-serine.

    abstract::A conformational study of poly-L-serine has shown that it can exist in the left-handed α-helical form. A study of a pair of peptide units with the serine sidegroup attached to the α carbon atom linking the two units showed that OH ⃛O hydrogen bonds between the OH group of the side chain and a carbonyl oxygen of the f...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.1968.360060403

    authors: Sarathy KP,Ramachandran GN

    更新日期:1968-04-01 00:00:00

  • Development of a chitosan-based nanoparticle formulation for delivery of a hydrophilic hexapeptide, dalargin.

    abstract::Nanoparticle based delivery systems can offer opportunities for targeting, controlled release, and enhanced stability of their drug, protein, or gene therapy payload. This study investigated the use of chitosan in combination with the ionic additives sulfobutyl-ether-7-beta-cyclodextrin (SB-CD) or SB-CD/dextran sulfat...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.21055

    authors: Chen Y,Siddalingappa B,Chan PH,Benson HA

    更新日期:2008-01-01 00:00:00

  • The secondary structure of turkey gizzard myosin light chain kinase and the nature of its interaction with calmodulin.

    abstract::The enzymatic activities of native myosin light chain kinases are subject to modification by interaction with Ca2(+)-calmodulin (CaM). The interaction between myosin light chain kinase isolated from turkey gizzard (tgMLCK) and calmodulin isolated from bovine testes (CaMbt) and wheat germ (CaMwg) has been examined by m...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.360301113

    authors: Garone L,Albaugh S,Steiner RF

    更新日期:1990-01-01 00:00:00

  • Structural changes in cartilage and collagen studied by high temperature Raman spectroscopy.

    abstract::Understanding the high temperature behavior of collagen and collagenous tissue is important for surgical procedures and biomaterials processing for the food, pharmaceutical, and cosmetics industries. One primary event for proteins is thermal denaturation that involves unfolding the polypeptide chains while maintaining...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.23017

    authors: Fields M,Spencer N,Dudhia J,McMillan PF

    更新日期:2017-06-01 00:00:00

  • Peptide helices based on alpha-amino acids.

    abstract::Relevant parameters and stereochemical consequences of helices [alpha-helix, 3(10)-helix, beta-bend ribbon spiral, gamma-helix, 2.0(5)-helix, poly(Pro)(n) type-I and -II helices, and collagen triple helix] of peptides based on alpha-amino acids for use as templates in various branches of chemistry are briefly discusse...

    journal_title:Biopolymers

    pub_type: 杂志文章,评审

    doi:10.1002/bip.20357

    authors: Crisma M,Formaggio F,Moretto A,Toniolo C

    更新日期:2006-01-01 00:00:00

  • Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity?

    abstract::Molecular dynamics (MD) simulations on stem loop 2 of U1 small nuclear RNA and a construct of the U1A protein were carried out to obtain predictions of the structures for the unbound forms in solution and to elucidate dynamical aspects of induced fit upon binding. A crystal structure of the complex between the U1A pro...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.10251

    authors: Pitici F,Beveridge DL,Baranger AM

    更新日期:2002-12-15 00:00:00

  • Terminal sidechain packing of a designed beta-hairpin influences conformation and stability.

    abstract::While end capping in alpha-helices is well understood, the concept of capping a beta-hairpin is a relatively recent development; to date, favorable Coulombic interactions are the only example of sidechains at the termini influencing the overall stability of a beta-hairpin. While cross-strand hydrophobic residues gener...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.21177

    authors: Eidenschink L,Crabbe E,Andersen NH

    更新日期:2009-07-01 00:00:00

  • Conformational preferences and synthesis of isomers Z and E of oxazole-dehydrophenylalanine.

    abstract::Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isome...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.22852

    authors: Staś M,Bujak M,Broda MA,Siodłak D

    更新日期:2016-05-01 00:00:00

  • Solution effects on the self-association of a water-soluble peptoid.

    abstract::A desire to replicate the structural and functional complexity of proteins with structured, sequence-specific oligomers motivates study of the structural features of water-soluble peptoids (N-substituted glycine oligomers). Understanding the molecular-level details of peptoid self-assembly in water is essential to adv...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.23248

    authors: Fuller AA,Huber J,Jimenez CJ,Dowell KM,Hough S,Ortega A,McComas KN,Kunkel J,Asuri P

    更新日期:2019-04-01 00:00:00

  • General properties of silated hydroxyethylcellulose for potential biomedical applications.

    abstract::The general properties of hydroxyethylcellulose (HEC) grafted with 3-glycidoxypropyltrimethoxysilane (GPTMS) or 3-glycidoxypropylmethyldiethoxysilane (GPDMS) were studied for potential biomedical applications. The graft involved a Williamson reaction between the free hydroxyl function of HEC and the epoxy function of ...

    journal_title:Biopolymers

    pub_type: 杂志文章

    doi:10.1002/bip.10053

    authors: Bourges X,Weiss P,Coudreuse A,Daculsi G,Legeay G

    更新日期:2002-04-05 00:00:00