Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization

Giovanni Smaldone, Rita Berisio, Nicole Balasco, Sabato D'Auria, Luigi Vitagliano, Alessia Ruggiero

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP20-233) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins.

Original languageEnglish
Pages (from-to)952-962
Number of pages11
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1866
Issue number9
DOIs
Publication statusPublished - Sep 1 2018

Fingerprint

Thermotoga maritima
Dissection
Arginine
Carrier Proteins
Ligands
Proteins
Chemical stability
Scaffolds
Structural properties
Thermodynamic stability
Hot Temperature
Observation
Peptides

Keywords

  • Argininemia diagnosis
  • Biosensors
  • Calorimetry
  • Domain swapping
  • Protein structure-stability

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

Domain swapping dissection in Thermotoga maritima arginine binding protein : How structural flexibility may compensate destabilization. / Smaldone, Giovanni; Berisio, Rita; Balasco, Nicole; D'Auria, Sabato; Vitagliano, Luigi; Ruggiero, Alessia.

In: Biochimica et Biophysica Acta - Proteins and Proteomics, Vol. 1866, No. 9, 01.09.2018, p. 952-962.

Research output: Contribution to journalArticle

Smaldone, Giovanni ; Berisio, Rita ; Balasco, Nicole ; D'Auria, Sabato ; Vitagliano, Luigi ; Ruggiero, Alessia. / Domain swapping dissection in Thermotoga maritima arginine binding protein : How structural flexibility may compensate destabilization. In: Biochimica et Biophysica Acta - Proteins and Proteomics. 2018 ; Vol. 1866, No. 9. pp. 952-962.
@article{88401ed38b4f46bc90225f4c9f6e12e1,
title = "Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization",
abstract = "Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP20-233) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins.",
keywords = "Argininemia diagnosis, Biosensors, Calorimetry, Domain swapping, Protein structure-stability",
author = "Giovanni Smaldone and Rita Berisio and Nicole Balasco and Sabato D'Auria and Luigi Vitagliano and Alessia Ruggiero",
year = "2018",
month = "9",
day = "1",
doi = "10.1016/j.bbapap.2018.05.016",
language = "English",
volume = "1866",
pages = "952--962",
journal = "Biochimica et Biophysica Acta - Proteins and Proteomics",
issn = "1570-9639",
publisher = "Elsevier",
number = "9",

}

TY - JOUR

T1 - Domain swapping dissection in Thermotoga maritima arginine binding protein

T2 - How structural flexibility may compensate destabilization

AU - Smaldone, Giovanni

AU - Berisio, Rita

AU - Balasco, Nicole

AU - D'Auria, Sabato

AU - Vitagliano, Luigi

AU - Ruggiero, Alessia

PY - 2018/9/1

Y1 - 2018/9/1

N2 - Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP20-233) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins.

AB - Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP20-233) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins.

KW - Argininemia diagnosis

KW - Biosensors

KW - Calorimetry

KW - Domain swapping

KW - Protein structure-stability

UR - http://www.scopus.com/inward/record.url?scp=85048156142&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85048156142&partnerID=8YFLogxK

U2 - 10.1016/j.bbapap.2018.05.016

DO - 10.1016/j.bbapap.2018.05.016

M3 - Article

AN - SCOPUS:85048156142

VL - 1866

SP - 952

EP - 962

JO - Biochimica et Biophysica Acta - Proteins and Proteomics

JF - Biochimica et Biophysica Acta - Proteins and Proteomics

SN - 1570-9639

IS - 9

ER -