Thermostability, the summary

Ronald Knegtel ronald at rugcbf.chem.rug.nl
Wed Jul 12 10:55:01 EST 1995


Dear netters,

as requested I send you a summary of the replies I got. 
An interesting review by A. Fontana (How nature engineers protein
(thermo) stability) in "Life under extreme conditions" Springer
Verlag Berlin Heidelberg 1991, Guido di Prisco (Ed.), pp. 89-113.

As for the rest of the responses...it's quite a long list

Here we go:

Look up Chan et al. (1995).Structure of a hyperthemophilic 
tunstopterin enzyme, ferredoxin oxidoreductase. Science 267:1463-1469.
Would you please send a summary of the answers you get to this mailing 
list. Since I am also working on a thermophilic enzyme I would be 
interested in that.
                      Regards,
                                     Menachem Shoham
                             Case Western Reserve University

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We are also working on a protein from an extreme thermophile which
likes to grow at 87C. We have just solved the structure, and the
first obvious thing is the presence of a lot of salt-bridges 
criss-crossing the protein surface. This phenomenon has been
noted previously by Mike Danson and Garry Taylor at the
University of Bath. I know Mike Danson has given a lot of talks
about protein thermostability, but I dont know if he has written any
reviews. You could just look his name up on Medline or some other 
computer bibliography system.

&

My physical chemistry friends (I have one or two, but they are sad creatures)
tell me that the free energy difference between a protein that denatures at 45
degrees and a protein that denatures at 95 degrees is only a few Kcal/mole,
equivalent to one or two hydrogen bonds !! If that really is he case, we will
all go very mad trying to understand thermostability.

Much more interesting is thermophilicity which is a common property of enzymes
from extreme and hyper (>100 degrees) thermophiles. This means that the enzyme
doesn't work until it reaches the high temperature !. I think this is quite 
different from moderate thermophiles such B.stearothermophilus etc.

Presumably the enzyme is very rigid at normal temperatures, but it isn't clear
whether the greater rate at the higher optimal temperature is due to easier
substrate binding in a more flexible active site, or to better chemical
catalysis. The other thing that worries me is how specificity is maintained at
very high temperatures.

There is a good thermophile protein meeting in London this Autumn. If you are
interested I will try and find the details.

Laurence Pearl


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+  Laurence Pearl                                                            +
+                                                                            +
+  Section of Structural Biochemistry                                        +
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The reference is:

The crystal structure of citrate synthase from the
thermophilic archaeon, Thermoplasma
acidophilum. 

Russell RJ; Hough DW; Danson MJ; Taylor GL 

School of biology and Biochemistry, University of Bath, UK. 

Structure 2: 1157-67 (1994) 

Some other references I got from medline and which seemed interesting:

Nature 324, 695-7 (1986)
Proteins 5:22-37, 1989
Protein Eng. 1:477-80 (1987)
"         "  4:11-33 (1990)
"         " 165-70 (1992)
Biochemistry 32: 3913-22 (1993)


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recent: dc rees & mww adams, structure 3, 251-254 (1995)
not-so-recent, but several references to earlier work
are in: gj davies et al, proteins 15, 283-289 (1993)

--gerard kleijwegt   

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i've done a bit of reading on that topic since i have once been interested
in GAPDH from thermotoga maritima. actually i'm still interested, but
maybe a bit more confused now. i'll give you a list of articles i have looked 
at. it's not complete, but maybe you'll find something usefull. i'll leave
it up to you to sort yourself through this. have fun !

                                                       ingo

@article{ADWW_88_42 ,
     author    = {  T. Alber and  S. Dao-pin and  K. Wilson and  J.A. Woznia
                    k and  S.P. Cook and B.W. Matthews },
     title     = {  Contribution of hydrogen bonds of Thr 157 to the thermo
                    dynamic stability of phage T4 lysozyme.},
     year      =   1988,
     journal   = {  Nature ( London )},
     volume    = { 330},
     pages     = {  42--46 }}
     
@article{BHTW_77_328 ,
     author    = {  G. Biesecker and  J.I. Harris and  J.C. Thierry and  J.E.
                    Walker and A.J. Wonacott },
     title     = {  Sequences and structure of D-glyceraldehyde-3-phosphate
                     dehydrogenase from \textit{Bacillus stearothermophilus} .},
     year      =   1977,
     journal   = {  Nature ( London )},
     volume    = { 266 },
     pages     = {  328--333 }}
     
@article{DBM_90_198 ,
     author    = {  S. Dao-pin and  W.A. Baase and B.W. Matthews },
     title     = {  A mutant T4 lysozyme ( Val 131 -> Ala ) designed to 
                    increase thermostability by the reduction of strain within 
                    an
                    $\alpha$ helix },
     year      =   1990,
     journal   = {  Proteins : Struct. Funct. Genet.},
     volume    = { 7 },
     pages     = {  198--204 }}
     
@article{IKKM_93_85,
     author    = {  K. Ishikawa and  S. Kimura and  S. Kanaya and  K. Morika
                    wa and H. Nakamura },
     title     = {  Structural study of mutants of \textit{ Escherichia 
                    coli} ribonuclease {HI} with enhanced thermostability.},
     year      =   1993,
     journal   = {  Protein Engineering },
     volume    = { 6 },
     pages     = { 85--91 }}
     
@article{LKGJ_92_769 ,
     author    = {  A. Luyten and  C.M. Kay and  M. Gold and J.B. Jones },
     title     = {  Single amino acid substitutions can further increase 
                    thee stability of a thermophilic L-lactate dehydrogenase.},
     year      =   1992,
     journal   = {  Protein Engineering},
     volume    = { 5 },
     pages     = {  769--774 }}
     
@article{KNOB_93_3913 ,
     author    = {  C.A. Kelly and  M. Nishiyama and  Y. Ohnishi and 
                    T. Beppu and J.J. Birktoft },
     title     = {  Determinants of protein stability in the 1.9-{\AA} crystal 
                    structure of malate dehydrogenase from the thermophilic 
                    bacterium \textit{Thermus f\/lavus} },
     year      =   1993,
     journal   = {  Biochemistry },
     volume    = { 32 },
     pages     = {  3913--3922 }}
     
@article{NADM_91_9816 ,
     author    = {  H. Nicholson and  P.E. Anderson and  S. Dao-pin and B.W. 
                    Matthews },
     title     = { Analysis of  interactions between charged  side chains 
                   and the $\alpha$-helix dipole using designed thermostable 
                   mutants of phage {T}4 lysozyme },
     year      =   1991,
     volume    = { 30 },
     journal   =  { Biochemistry },
     pages     =  { 9816--9828 }} 
     
@article{NHON_78_33 ,
     author    = {  H. Nojima and  K. Hon-nami and  T. Oshima and H. Noda },
     title     = {  Reversible thermal unfolding of thermostable cytochrome
                     c-552.},
     year      =   1978,
     journal   = {  J. Mol. Biol.},
     volume    = { 122 },
     pages     = {  33--42 }}
     
@article{RJ_92_10999 ,
     author    = {  V. Rehaber and R. Jaenicke },
     title     = {  Stability and reconstitution of 
                    {d}-Glyceraldehyde-3-phosphate dehydrogenase from 
                    the hyperthermophilic bacterium 
                    \textit{{T}hermotoga maritima} },
     year      =   1992,
     journal   = {  J. Biol. Chem.},
     volume    = { 267},
     pages     = {  10999--11006 }}
     
@article{WSSJ_90_7584 ,
     author    = {  A. Wrba and  A. Schweiger and  V. Schultes and  
                    R. Jaenicke and P. Zavodsky },
     title     = {  Extremely thermostable {D}-glyceraldehyde-3-phosphate 
                    dehydrogenase from the eubacterium 
                    \textit{{T}hermotoga maritima} .},
     year      =   1990,
     journal   = {  Biochemistry },
     volume    = { 29 },
     pages     = {  7584--7592 }}
     
@article{ADWW_87_42,
    author    = { T. Alber  and S. Dao-pin  and K. Wilson and
                  J.A. Wozniak and S.P. Cook and B.W. Matthews },
    year      = 1987,
    title     = { Contribution of hydrogen bonds of {T}hr 157 to the 
                  thermodynamic stability of phage {T}4 lysozyme. },
    journal   = { Nature (London) },
    volume    = 330,
    pages     = { 41 -- 46 } }

@article{DBM_90_198,
    author    = { S. Dao-pin and W.A. Baase and B.W. Matthews },
    year      =  1990,
    title     = { A mutant {T}4 lysozyme ({V}al 131 . {A}la) designed 
                  to increase thermostability by the reduction of strain 
                  within an $\alpha$-helix. }, 
    journal   = { Proteins : Struct. Funct. Genet. },
    volume    = 7,
    pages     = { 198 -- 204 } }

@inproceedings{HC_76,
    author    = { Herbert and Codd },
    title     = { Role of calcium ions in the thermostability of amylase
                  produced by \textit{{B}ac. stearothermophilus}. },
    booktitle = { Proceedings of the international symposium on enzymes 
                  and proteins from thermophilic microorganisms, Z"urich. 
                  Structure and function. },
    year      = { 1976 },
    editor    = { Zuber, H. },
    publisher = { Birkhaeuser },
    address    = { Basel }}

@article{KSPM_92_769,
    author    = { H.K.W. Kallwass and W.K. Surewicz and W. Parris and
                  L.A. Macfarlane and A. Luyten and C.M. Kay and 
                  M. Gold and J.B. Jones },
    year      = 1992,
    title     = { Single amino acid substitutions can further increase 
                  the stability of a thermophilic {L}-lactate dehydrogenase. }, 
    journal   = { Protein Engineering },
    volume    = 5,
    pages     = { 769 -- 774 } }

@article{MKIA_84_413,
    author    = { Matsumura, M. and Katamura, Y. and Iwanaka, T. and Aiba, S. },
    year      = 1984,
    title     = {  Enzymatic and nucleotide sequence studies of a kanamycine
                   inactivating enzyme encoded by a plasmid from thermophilic
                   bacilli in comparison with that enzyme encoded by plasmid
                   pUB110 },
    journal   = {  J. Bacteriol. },
    volume    = 160,
    pages     = { 413 -- ??? } }

@article{WH_74_3215,
    author    = { Wedler, F.C. and Hof\/fmann, F.M. },
    year      = 1974 ,
    title     = { Glutaminesynthase of \textit{Bacillus stearothermophilus}.
                  {II}. Regulation and thermostability },
    journal   = { Biochemistry },
    volume    = 13 ,
    pages     = { 3215 -- 3221 } }

@article{WSSJ_90_195,
   author     = { Wrba, A. and Jaenicke, R. and Huber, R. and Stetter, K.O. },
   year       = 1990,
   title      = { Lactate dehydrogenase from the extreme thermophile
                  \textit{Thermotoga maritima}.},
   journal    = { Eur. Journ. Biochem. },
   volume     = { 188 },
   pages      = { 195 -- 201}}

@article{Y_76_91,
    author    = { K. Yutani},
    year      = 1976,
    title     = { Role of calcium ion in the thermostability of alpha amylase
                  produced from \textit{Bacillus stearothermophilus}. },
    journal   = { Experientia },
    volume    = { 26 },
    pages     = { 91 -- 103 }}

@article{KSHT_95_511,
   author     = { I. Kornd"orfer and B. Steipe and R. Huber and A. Tomschy
                  and R. Jaenicke },
   year       = 1995,
   title      = { The crystal structure of holo-glyceraldehyde-3-phosphate 
                  dehydrogenase from the hyperthermophilic {B}acterium 
                  \textit{Thermotoga maritima} at 2.5 {\AA} resolution },
   journal    = { J. Mol. Biol. },
   volume     = { 246 },
   pages      = { 511 -- 521 }}

@article{TBJ_94_9999,
     author    = {  A. Tomschy and  G. B"ohm and R. Jaenicke },
     title     = {  Ef\/fect of central and peripheral ion-pairs on the
                    thermal stability of D-glyceraldehyde-3- phosphate 
                    dehydrogenase. }, 
     year      =   1994,
     journal   = {  Eur. J. Biochem.},
     volume    = {??? },
     pages     = { ??? }}

@article{J_91_715 ,
     author    = { R. Jaenicke },
     title     = {  Protein stability and molecular adaptation to extreme 
                    conditions.},
     year      =   1991,
     journal   = {  Eur J. Biochem.},
     volume    = { 202 },
     pages     = {  715--728 }}


@article{AGSW_87_34,
    author    = { L. Achenbach-{R}ichter and R. Gupta and K.O. Stetter 
                  and C.R. Woese },
    year      = 1987,
    journal   = { System. Appl. Microbiol. },
    volume    = 9,
    pages     = { 34 -- 39 } }


@article{ARGZ_79_5698 ,
     author    = {  P. Argos and  M.G. Rossmann and  U.M. Grau and  H. Zuber
                     and  G. Frank and J. Tratschin },
     title     = {  Thermal stability and protein structure.},
     year      =   1979,
     journal   = {  Biochemistry },
     volume    = { 18 },
     pages     = {  5698--5703 }}
     
@article{MA_89_397 ,
     author    = {  L. Menendez-Arias and P. Argos },
     title     = {  Engineering protein thermal stability. {S}equence 
                    statistics point to residue substitutions in 
                    $\alpha$-helices.},
     year      =   1989,
     journal   = { J. Mol. Biol.}, 
     volume    = { 206 },
     pages     = {  397--406 }}



@book{B_78_1,
    author    = { T.D. Brock },
    title     = { Thermophilic Microorganisms and Life at High Temperatures },
    publisher = { Springer-Verlag},
    year      = 1978,
    address   = { New York, Heidelberg, Berlin },
    pages     = { 1 -- 11 } }

@incollection{TB_78_159,
    author    = { Tansey, M.R. and Brock, T.D. },
    year      = 1978,
    type      = { },
    title     = { Microbial life at high temperatures : 
                  {E}cological aspects }, 
    booktitle = { Microbial life in extreme environments },
    editor    = { Kushner, D.J. },
    publisher = { Academic Press },
    adress   = { London, New York, San Francisco },
    pages     = { 159 -- 216 } }


@article{BZR_90_411,
     author    = {  S. Brunie and C. Zelwer and J.-L. Riesler },
     title     = {  Crystallographic studies at 2.5 {\AA} resolution of the
                    interaction of methionyl-t{RNA} synthetase from 
                    \textit{E.coli}. },
     year      =   1990,
     journal   = { J. Mol. Biol.},
     volume    = { 216 },
     pages     = { 411--424 }}

@article{DSBW_91_221,
    author    = { S. Dao-pin and E. S"oderlind and W.A. Baase 
                  and J.A. Wozniak and U. Sauer and B.W. Matthews },
    year      =  1991,
    title     = { Cumulated site directed charge change replacements
                  in bacteriophage {T}4 lysozyme suggest that long-range 
                  electrostatic interactions contribute little to protein 
                  stability. },
    journal   =  { J. Mol. Biol.  },
    volume    =  221,
    pages     =  { 873 -- 887 } }


@article{DGLW_93_283 ,
     author    = {  G.J. Davies and  S.J. Gamblin and  J.A. Littlechild and
                    H.C. Watson },
     title     = {  The structure of a thermally stable 3-phosphoglycerate 
                    kinase and a comparison with its mesophilic equivalent.},
     year      =   1993,
     journal   = {  Proteins },
     volume    = { 15 },
     pages     = {  283--289 }}


@article{GP_90_9395 ,
     author    = {  C. Ganther and A. Pl"uckthun },
     title     = {  Gly to {A}la substitutions in helices of {GAPDH} : 
                    ef\/fects on stability.},
     year      =   1990,
     journal   = {  Biochemistry},
     volume    = { 29 },
     pages     = {  9395--9402 }}

@article{WWH_80_581 ,
     author    = {  J.E. Walker and  A.J. Wonacott and J.I. Harris },
     title     = {  Heat stability of a tetrameric enzyme, 
                    {d}-glyceraldehyde-3-phosphate dehydrogenase.},
     year      =   1980,
     journal   = {  Eur. J. Biochem.}, 
     volume    = { 108 },
     pages     = {  581--586 }}

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 http://www.biochem.mpg.de:70/research-groups/xray/usr/korndoer/ingo.html

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Joel Sussman has just published a paper on the structure of a thermostable
enzyme and he addresses the issue there (Science or Nature, this year)
-that would be a start

	Joe Mack
	mack at ncifcrf.gov


I hope this helps.



Ronald




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