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Showing NP-Card for L-Stachydrine (NP0045351)

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Record Information
Version2.0
Created at2022-03-17 19:18:26 UTC
Updated at2022-03-17 19:18:26 UTC
NP-MRD IDNP0045351
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Stachydrine
DescriptionProline betaine, also known as stachydrine or dimethylproline, belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. An amino acid betaine that is L-proline zwitterion in which both of the hydrogens attached to the nitrogen are replaced by methyl groups. Proline betaine is a moderately acidic compound (based on its pKa). Proline betaine exists in all living organisms, ranging from bacteria to humans. Outside of the human body, Proline betaine is found, on average, in the highest concentration within capers. Proline betaine has also been detected, but not quantified in, several different foods, such as limes, rices, corns, sweet oranges, and pulses. L-Stachydrine is found in Achillea collina, Achillea millefolium , Asphodelus microcarpus , Betonica officinalis , Boscia angustifolia, Capparis aegyptia , Capparis deserti, Capparis leucophylla, Capparis spinosa L. , Capparis tomentosa , Chaetomorpha ligustica, Citrus natsudaidai , Citrus unshiu , Combretum micranthum , Desmodium triflorum , Eremostachys speciosa, Erythrina variegata , Erythrochiton brasiliensis, Lagochilus inebrians Bge., Lagochilus pubescens, Lagochilus setulosus, Lamium album L. , Lamium maculatum, Leonurus heterophyllus , Leonurus sibiricus , Leonurus turkestanicus, Cudrania tricuspidata , Gymnosporia senegalensis, Phlomoides tuberosa, Sabia schumanniana, Stachys balansae, Stachys betoniciflora, Stachys betonicifolia, Stachys hissarica, Stachys lanata, Stachys tuberifera, Stachys tubifera, Teucrium polium and Urtica cannabina . L-Stachydrine was first documented in 1984 (PMID: 6372974). This could make proline betaine a potential biomarker for the consumption of these foods (PMID: 3546377) (PMID: 8068711) (PMID: 18060588) (PMID: 24704554) (PMID: 25012968).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0045351 (L-Stachydrine)


  Mrv1652309121709222D          

 10 10  0  0  1  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  2 10  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
Download

3D MOL for NP0045351 (L-Stachydrine)

     RDKit          3D

 23 23  0  0  0  0  0  0  0  0999 V2000
   -1.2830   -1.3089   -0.7730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5250   -0.2307   -0.1177 N   0  0  2  0  0  4  0  0  0  0  0  0
   -1.0293   -0.1168    1.2117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6765    1.0144   -0.8406 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4010    1.8820   -0.2294 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5151    0.8894    0.0291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8775   -0.4652   -0.2206 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3985   -1.5046    0.6730 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2073   -2.7132    0.3777 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0892   -1.2320    1.8234 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.3695   -1.1040   -0.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0690   -1.2999   -1.8633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9869   -2.2576   -0.2861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1468   -0.1198    1.1478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7452    0.8202    1.7269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7501   -0.9568    1.8471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6727    1.4491   -0.7699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3560    0.8081   -1.8903 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7293    2.6944   -0.9341 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0636    2.3913    0.6884 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9081    0.9721    1.0698 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3229    1.1013   -0.7176 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0975   -0.7127   -1.2893 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8 10  1  0
  8  9  2  0
  7  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
  7 23  1  6
M  CHG  2   2   1  10  -1
M  END
Download

3D SDF for NP0045351 (L-Stachydrine)


  Mrv1652309121709222D          

 10 10  0  0  1  0            999 V2000
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  2 10  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
> <DATABASE_ID>
NP0045351

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+]1(C)CCC[C@H]1C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/t6-/m0/s1

> <INCHI_KEY>
CMUNUTVVOOHQPW-LURJTMIESA-N

> <FORMULA>
C7H13NO2

> <MOLECULAR_WEIGHT>
143.1836

> <EXACT_MASS>
143.094628665

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.05016181177956

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1,1-dimethylpyrrolidin-1-ium-2-carboxylate

> <ALOGPS_LOGP>
-2.24

> <JCHEM_LOGP>
-3.8764300881384117

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.258526077274334

> <JCHEM_POLAR_SURFACE_AREA>
40.129999999999995

> <JCHEM_REFRACTIVITY>
60.10970000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
stachydrine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0045351 (L-Stachydrine)

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PDB for NP0045351 (L-Stachydrine)
HEADER    PROTEIN                                 12-SEP-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-17         0                                  
HETATM    1  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.060   2.080   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.795   0.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O-1
HETATM   10  C   UNK     0       2.090   3.224   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6   10                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    2                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0045351 (L-Stachydrine)
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SMILES for NP0045351 (L-Stachydrine)
C[N+]1(C)CCC[C@H]1C([O-])=O
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INCHI for NP0045351 (L-Stachydrine)
InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/t6-/m0/s1
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View in JSmol
Synonyms
ValueSource
(S)-2-Carboxylato-1,1-dimethylpyrrolidiniumChEBI
N,N-Dimethyl-L-prolineChEBI
StachydrineChEBI
L-Proline betaineKegg
DimethylprolineHMDB
Stachydrine chloride, (S)-isomerHMDB
Stachydrine chlorideHMDB
Stachydrine, (+-)-isomerHMDB
(2S)-2-Carboxy-1,1-dimethylpyrrolidiniumHMDB
(S)-2-Carboxy-1,1-dimethylpyrrolidiniumHMDB
HomostachydrineHMDB
Prestwick-08g03HMDB
Proline betaineChEBI
Chemical FormulaC7H13NO2
Average Mass143.1836 Da
Monoisotopic Mass143.09463 Da
IUPAC Name(2S)-1,1-dimethylpyrrolidin-1-ium-2-carboxylate
Traditional Namestachydrine
CAS Registry Number471-87-4
SMILES
C[N+]1(C)CCC[C@H]1C([O-])=O
InChI Identifier
InChI=1S/C7H13NO2/c1-8(2)5-3-4-6(8)7(9)10/h6H,3-5H2,1-2H3/t6-/m0/s1
InChI KeyCMUNUTVVOOHQPW-LURJTMIESA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Achillea collinaLOTUS Database
Achillea millefoliumPlant
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Asphodelus microcarpusPlant
Betonica officinalisPlant
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Boscia angustifoliaLOTUS Database
Bubalus bubalisFooDB
Capparis aegyptiaPlant
Capparis desertiPlant
Capparis leucophyllaPlant
Capparis spinosaFooDB
Capparis spinosa L.Plant
Capparis tomentosaPlant
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
Chaetomorpha ligusticaLOTUS Database
Citrus aurantiifoliaFooDB
Citrus limonFooDB
Citrus maximaFooDB
Citrus natsudaidaiPlant
Citrus paradisiFooDB
Citrus reticulataFooDB
Citrus unshiuPlant
Citrus X sinensis (L.) Osbeck (pro. sp.)FooDB
ColumbaFooDB
ColumbidaeFooDB
Combretum micranthumPlant
Desmodium triflorumPlant
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Eremostachys speciosaPlant
Erythrina variegataPlant
Erythrochiton brasiliensisLOTUS Database
Gallus gallusFooDB
Lagochilus inebrians Bge.Plant
Lagochilus pubescensPlant
Lagochilus setulosusPlant
Lagopus mutaFooDB
Lamium albumPlant
Lamium maculatumLOTUS Database
Leonurus japonicusPlant
Leonurus sibiricusPlant
Leonurus turkestanicusPlant
LeporidaeFooDB
Lepus timidusFooDB
Maclura tricuspidataPlant
Maytenus senegalensisLOTUS Database
Medicago sativaFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Phlomoides tuberosaLOTUS Database
Sabia schumannianaPlant
Stachys balansaePlant
Stachys betonicifloraPlant
Stachys betonicifoliaPlant
Stachys hissaricaPlant
Stachys lanataPlant
Stachys tuberiferaPlant
Stachys tubiferaPlant
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Teucrium poliumLOTUS Database
Urtica cannabinaPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentProline and derivatives  
Alternative Parents
Substituents
  • Proline or derivatives
    • 

  • Alpha-amino acid
    • 

  • L-alpha-amino acid
    • 

  • Pyrrolidine carboxylic acid
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • N-alkylpyrrolidine
    • 

  • Tetraalkylammonium salt
    • 

  • Pyrrolidine
    • 

  • Quaternary ammonium salt
    • 

  • Carboxylic acid salt
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Amine
    • 

  • Carbonyl group
    • 

  • Organic salt
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.2ALOGPS
logP-3.9ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)2.26ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area40.13 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity60.11 m³·mol⁻¹ChemAxon
Polarizability15.05 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0004827  
DrugBank IDDB04284  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB000463  
KNApSAcK IDC00002074  
Chemspider ID103115  
KEGG Compound IDC10172  
BioCyc IDCPD-821  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7089  
PubChem Compound115244  
PDB IDNot Available
ChEBI ID35280  
Good Scents IDNot Available
References
General References
  1. Chambers ST, Kunin CM: Isolation of glycine betaine and proline betaine from human urine. Assessment of their role as osmoprotective agents for bacteria and the kidney. J Clin Invest. 1987 Mar;79(3):731-7. [PubMed:3546377  ] 
  2. Le Rudulier D, Bernard T, Goas G, Hamelin J: Osmoregulation in Klebsiella pneumoniae: enhancement of anaerobic growth and nitrogen fixation under stress by proline betaine, gamma-butyrobetaine, and other related compounds. Can J Microbiol. 1984 Mar;30(3):299-305. doi: 10.1139/m84-045. [PubMed:6372974  ] 
  3. Lever M, Sizeland PC, Bason LM, Hayman CM, Chambers ST: Glycine betaine and proline betaine in human blood and urine. Biochim Biophys Acta. 1994 Aug 18;1200(3):259-64. doi: 10.1016/0304-4165(94)90165-1. [PubMed:8068711  ] 
  4. Atkinson W, Downer P, Lever M, Chambers ST, George PM: Effects of orange juice and proline betaine on glycine betaine and homocysteine in healthy male subjects. Eur J Nutr. 2007 Dec;46(8):446-52. doi: 10.1007/s00394-007-0684-5. Epub 2007 Dec  4. [PubMed:18060588  ] 
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