Name: Cláudio
Manuel Soares
Date of birth: 1966-08-24
Mail address:
Instituto
de Tecnologia Química e Biológica
Universidade
Nova de Lisboa
Av. da
República, Apartado 127
2781-901
Oeiras
Portugal
Telephone: +351 21 4469610
Fax:
+351 21 441 1277
Email: claudio@itqb.unl.pt
WWW: http://www.itqb.unl.pt/~claudio
- PhD in Biochemistry
(theoretical/computational) - 1994 -
-
Filosofie Licentiatexamen
- 1994 - Department of Physical Chemistry,
- Licenciatura in
Biochemistry - 1989 -Department of
Chemistry, Faculdade de Ciências
da Universidade
de Lisboa. Final classification of 17
(scale 0-20). This
Portuguese degree is higher than a BSc.
Main scientific field: Molecular modelling of biomolecules
Current research interests: His scientific interests
are centred in
applications and development of molecular modelling techniques and
their
interactions with experimental techniques related with biomolecular
structure and function. Some of the main scientific problems currently
studied
in his laboratory include mechanisms involving redox
proteins and redox processes, protein
structure
prediction, enzyme structure, dynamics and catalysis in non-aqueous
media,
studies of proteins involved in human disease, and methodological
developments
in biomolecular modelling methods.
4-Positions
(in reverse order)
- March 2005 to present day – Associate Professor at
the Instituto de Tecnologia
Química e Biológica, Universidade Nova de Lisboa.
- February 1999 to present day -
Leader of the
Protein Modelling Laboratory
at the Instituto de Tecnologia
Química e Biológica,
Universidade Nova de Lisboa.
Present
research staff of the Protein Modelling Group:
-Bruno Victor, Post-Doc
-Ana Sofia Oliveira, PhD
student
-Diana Lousa, PhD student
-João
Damas, Research student
Former members include:
-Nuno
Micaêlo,
former PhD student, now a post-doc at Universidade
de
Aveiro
-Carlos A. Cunha, former
Post-Doc, now working at DHL
-Zélia
Ferreira, Research
student, now a research student at Universidade
do
-Vitor
Hugo Teixeira, former PhD student, now a
post-doc at Universidade do
-Paulo J. Martel, PhD,
Assistant Prof. at Universidade do
-António
M. Baptista, PhD, former post-doc, now a
group leader at
ITQB-UNL
-Joaquim
Mendes, former PhD
student, now a group leader at the Max Planck Institute of Molecular
Physiology,
-Nuno
Elias, BSc, former
Diploma student, now a Wine Engineer
- June 2005 to February
2008 – Vice-Director of the
Instituto de Tecnologia Química e Biológica, Universidade Nova de
Lisboa.
- February 1999 February
2005 - Invited
Assistant Professor at
the Instituto de Tecnologia Química e
Biológica,
Universidade Nova de Lisboa.
Vice-Director of the
Instituto de Tecnologia Química e Biológica, Universidade Nova de
Lisboa. From June 2005 to February
2008.
Chairman of the Portuguese
Biophysical
Society. From
December 2002 to
the present day.
Member of the directing board of the Portuguese
Biophysical Society. From 1998 to the end of 2002.
Member of the Co-ordinating Committee of the
Scientific Council of the
Instituto de Tecnologia
Química e Biológica,
Universidade Nova de Lisboa.
From 1999 to February 2008.
Member of the organising
committee of
the Chemical and Biological Sciences
PhD program of ITQB-UNL.
From 2003 to 2006.
Deputy Director of the Gulbenkian PhD Program
in Computational
Biology. From 2007 to the present day.
Supervision of PhD students: Responsible for four PhD
students that
have finished and three PhD students currently doing their research.
Supervision of Diploma students: Responsible for five
Diploma students
that have finished.
Supervision of Research students: Responsible for seven
research students,
six of which have become PhD students meanwhile.
Teaching activities in PhD
programs: Biomolecular
modelling techniques in the ITQB-UNL PhD program (in the years of 1999,
2003, 2004,
2005 and 2006). Biomolecular
modelling techniques in the Gulbenkian PhD
program in
biology and medicine (in the years of 1997, 1998, 1999, 2000 and 2001).
Molecular modelling methodologies in the Gulbenkian
Program in Computational Biology: co-coordinator of the submodule
MSS2: Structures (DNA, RNA and proteins), lasting for three continuous
weeks –
2005, 2006 and 2008. Protein structure prediction methodologies in the
Bioinformatics course of the International Postgraduate programme from Universidade do
Teaching activities in Master programs: Biomolecular
modelling techniques in the Master degree in Biophysics of the
i) Principal researcher in the
PRAXIS XXI/JNICT
(PBICT/BIO/2037/95) project “Molecular modelling of proteins involved
in
electron transfer processes”). January 1996 - December 1998.
ii) Responsible for the protein
modelling
activities in the JNICT Luso-Hungariun
project “
iii)
Responsible
for the protein modelling activities in the PRAXIS XXI project
“Structural
determinants of electron transfer interactions between [Ni-Fe] hydrogenase and cytochrome
c3
from D.desulfuricans ATCC 27774”. 1997-1998.
iv)
Responsible
for the
protein modelling activities in the PRAXIS XXI project “Structural
determination of proteins using X-ray crystallography and its
structural
implications".1997-1998.
v)
Responsible
for the protein modelling activities in the EC BIOTECNOLOGY PROGRAM
AREA 6.1
project (BIO4-CT96-0413) “Construction of novel redox
proteins from modular building blocks”. November 1996 - October 1999.
vi)
Responsible
for the
protein modelling activities in the PRAXIS XXI project
PRAXIS/P/BIO/14314/1998
“Structure function relationships of serine hydrolases
in non-conventional media”. October 2000 - September 2002.
vii)
Principal
researcher in the FCT Sapiens project POCTI/BME/32789/99 entitled
"Molecular modelling of key redox proteins
in
bacterium metabolism: methodology and applications". July 2001- June
2004.
viii)
Responsible
for the protein modelling activities in the FCT Sapiens project
POCTI/BME/32789/99 entitled "Novel respiratory complexes: molecular
basis
for energy transduction". 2001-2003.
ix)
Responsible
for the protein modelling activities in the FCT Sapiens
POCTI/QUI/43323/2001
project entitled "Electron transfer mechanisms and dynamics of a proton
thruster: cytochrome
c3". 2001-2004.
x)
Responsible
for the protein modelling activities in the FCT Sapiens
POCTI/MGI/47382/2002
project entitled "Folding, processing and function of normal and mutant
cystic fibrosis transmembranar conductance
regulator:
structural implications". 2002-2005.
xi)
Involved in
the FCT Sapiens POCTI/BME/45810/2002 project entitled “Increasing
realism in
protein modelling: including pH and redox
effects
into molecular dynamics simulations”. 2003-2006.
xii)
Responsible
for the protein modelling activities in the FCT Sapiens
POCTI/BIO/57083/2004
project entitled “Nano-engineering of
bacterial laccases”. 2005-2008.
xiii)
Responsible
for the protein modelling activities in the FCT Sapiens
POCTI/BIO/57193/2004
project entitled “Rationalization of cutinase
enantioselectivity in nonaqueous
media”. 2005-2008
xiv)
Responsible
for the protein modelling activities at the ITQB-UNL partner of the EU
FP6-2004-NMP-NI-4/02456 IP project. “White
biotechnology for
added value products from renewable plant polymers: Design of
tailor-made
biocatalysts and new industrial bioprocesses” (acronym BIORENEW). 2006-2010
xv)
Responsible
for the protein modelling activities in the FCT project
PTDC/BIA-PRO/70429/2006. “Towards biohydrogen
production – study of a high-activity, oxygen-resistant bacterial hydrogenase”. 2007-2010
xvi)
Responsible
for the protein modelling activities in the FCT project
PTDC/BIA-PRO/XXXXX/2006. “Microbial enzymes involved in superoxide
and nitric oxide reduction”. 2008-2010
i) Biopolymers - In the year
of 1999.
ii)
Proteins - In
the years of 2000 and 2004.
iii)
Biophysical
Journal - In the year of 2002.
iv)
Journal of
Biological
Inorganic Chemistry- In the years of 2002 and 2003.
v)
Protein
Science - In the years of 2003 and 2004.
vi)
Journal of
Computational Chemistry - In the year of 2003.
vii)
FEBS Letters
– In the years of 2005 and 2006
viii)
Journal of
Cystic Fibrosis - In the year of 2004.
ix)
Protein
Engineering Design and Selection – In the year of 2005
x)
Biophysics
(Biophysical Society of Japan) – In the year of 2006
xi)
Journal of
Chemical Physics – In the year of 2006
xii)
Journal of
Biotechnology – In the year of 2006
xiii)
Journal of
Physical Chemistry – In the year of 2006
xiv)
BMC
Biotechnology – In the year of 2006
xv)
Journal of
Molecular Graphics and Modelling – In the year of 2006
xvi)
Chemical
Physics Letters – In the year of 2006
xvii)
Extremophiles – In the year of 2007
9-Publications
in ISI peer-reviewed journals
1)
Björkstén, J, Soares,
CM, Nilsson, O, Tapia, O (1994) “On the stability and plastic
properties of the
interior L3 loop in R.capsulatus
porin. A molecular
dynamics study.”
Protein Engineering, 7, 487-493
2) Soares,
CM, Björkstén, J,
Tapia, O (1995) “Perturbation-relaxation molecular dynamics simulations
as a
tool to explore conformational space. Reversible
response of
the L3 loop in porin towards charge
screening
effects”. Molecular Simulation,
15, 35-46
3) Soares,
CM, Björkstén, J, Tapia,
O (1995) “L3-loop mediated mechanisms of pore closing in porin.
A molecular dynamics perturbation approach”.
Protein Engineering, 8, 5-12
4) Frazão,
C, Soares, CM, Carrondo,
MA, Pohl, E, Dauter, Z,
Wilson, KS, Hervás, M, Navarro, JA, De la
Rosa, MA, Sheldrick, GM (1995) ”Ab initio determination of the crystal
structure of cytochrome c6
from the green algae Monoraphidium braunii.”, Structure,
3, 1159-1169
5) Soares,
CM, Martel, PJ,
6) Soares,
CM, Martel, PJ, Mendes, J,
7) Fontes,
N, Almeida, MC, Peres, C, Garcia, S, Grave, J,
Aires-Barros, MR, Soares,
CM, Cabral, JMS, Maycock, CD, Barreiros,
S (1998) ”Cutinase activity and enantioselectivity
in supercriticalfluids”, Ind.Eng.Chem.Res.,
37,
3189-3194
8) Mendes, J, Soares, CM, Carrondo,
MA
(1999) “Improvement of side-chain modelling in proteins with the
Self-Consistent Mean Field Theory method based on an analysis of the
factors
influencing prediction”, Biopolymers,
50, 111-131
9) Petukhov,
M, Cregut, D, Soares,
CM, Serrano, L (1999) “Local water bridges
and protein conformational stability”, Prot.Sci., 8, 1982-1989
10) Martel, PJ, Soares, CM, Baptista,
AM, Fuxreiter, M, Náray-Szabó,
G, Louro, RO,
11) Baptista,
AM, Martel, PJ, Soares,
CM (1999) “Simulation of electron-proton coupling with a
12)
13) Mendes, J, Baptista, AM and
14)
15) Burke, DF,
Deane, CM, Nagarajaram, HA, Campillo,
N, Martin-Martinez, M, Mendes, J, Molina, F, Perry, J, Reddy, BVB, Soares, CM, Steward, RE, Williams, M, Carrondo, MA, Blundell, TL, Mizuguchi,
K (1999) “An iterative structure-assisted approach to sequence
alignment and
comparative modelling”, Proteins, Suppl 3, 55-60
16) Matias,
PM, Saraiva, LM, Soares,
CM, Coelho, AV, LeGall,
J, Carrondo, MA (1999) “Nine-haem
cytochrome c from Desulfovibrio
desulfuricans ATCC 27774: primary sequence
determination, crystallographic refinement at 1.8Å and modelling
studies of its
interaction with the tetrahaem cytochrome
c3 from the same
organism”, JBIC, 4, 478-494
17) Frazão,
C, Bento, I, Costa, J, Soares,
CM, Veríssimo, P, Faro, C, Pires,
E, Cooper, J, Carrondo, MA (1999) “Crystal
structure
of cardosin A, a glycosylated
and Arg-Gly-Asp containing aspartic proteinase from the flowers of Cynaracardunculus L.”,
J.Biol.Chem.,
274, 27694-27701
18) Power, DM, Elias, NP,
19) Sadeghi,
SJ, Valetti, F, Cunha,
CA, Romão, MJ, Soares,
CM, Gilardi, G
(2000) "Ionic strength dependence of the non-physiological electron
transfer between flavodoxin and cytochrome
c553 from D.vulgaris.",
JBIC, 5, 730-737
20) Matias,
PM, Soares, CM, Saraiva, LM, Coelho, R, Morais,
J, LeGall, J,
21) Baptista,
AM, Soares, CM
(2001) "Some theoretical and computational aspects of the inclusion of
proton isomerism in the protonation
equilibrium of
proteins", J.Phys.Chem.B,
105, 293-309
22) Santana, M,
23)
24) Mendes, J, Nagarajaram, HA, Soares,
CM, Blundell, TL,
25) Mendes, J, Baptista, AM,
26)
27) Louro,
RO, Bento, I, Matias, PM, Catarino, T, Baptista,
AM, Soares, CM, Carrondo, MA,
Turner, DL, Xavier, AV (2001) " Conformational component in the coupled
transfer of multiple electrons and protons in a monomeric
tetrahaem cytochrome",
J.Biol.Chem.,
276,
44044-44051
28) Teixeira,
VH, Soares, CM, Baptista, AM (2002) "Studies of the reduction
and protonation behaviour of tetrahaem
cytochromes using atomic detail", JBIC, 7, 200-216
29) Martins, LO, Soares, CM,
30) Baptista,
AM, Teixeira, VH, Soares,
CM (2002) "Constant-pH molecular
dynamics using stochastic titration", J.Chem.Phys., 117, 4184-4200
31) Soares,
CM, Teixeira, VH, Baptista,
AM (2003) "Protein structure and dynamics in
nonaqueous solvents. Insights from
molecular dynamics
simulation studies", Biophys.J.,
84, 1628-1641
32) Victor, BL
Vicente, JB, Rodrigues, R, Oliveira, S, Rodrigues-Pousada, C, Frazão,
C,
Gomes, CM, Teixeira, M, Soares,
CM (2003) "Docking and Electron Transfer Studies between Rubredoxin and Rubredoxin:Oxygen Oxidoreductase",
JBIC, 8, 475-488
33) Bento, I, Teixeira, VH, Baptista,
AM, Soares, CM, Matias, PM,
34)
35) Bento, I, Matias, PM, Baptista,
AM, da Costa, PN, van Dongen,
WMAM, Saraiva, LM, Schneider, TR, Soares,
CM, Carrondo, MA (2004) "Molecular basis
for redox-Bohr and cooperative effects in cytochrome
c3 from Desulfovibrio desulfuricans
ATCC 27774: crystallographic and modelling studies of oxidised and
reduced high
resolution structures at pH 7.6", Proteins,
54, 135-152
36) Vidinha,
P, Harper, N, Micaelo,
NM, Lourenço, N, Richter, M, Cabral, JMS, Afonso, C, Soares,
CM, Barreiros, S (2004) "Effect of
immobilization support,
water activity and enzyme ionization state on cutinase
activity and enantioselectivity in organic
media", Biotech. Bioeng., 85,
442-449
37) Soares,
CM, Baptista, AM,
38) Teixeira,
VH, Baptista, AM, Soares,
CM (2004) “Modelling electron transfer
thermodynamics in protein complexes: interaction between two cytochromes c3", Biophys.J., 86, 2773-2785
39) Serrano, M, Neves, A, Soares,
CM,
Moran, CP, Henriques, AO (2004) “Role of
the
anti-sigma factor SpoIIAB in the
regulation of sG
during Bacillus
subtilis sporulation”,
J.Bacteriology, 186,
4000-4013
40) Victor, BL, Baptista, AM, Soares,
CM
(2004) "Study of proton channels in the aberrant Quinol
Oxidase aa3
from Acidianus
ambivalens: a
novel approach combining comparative modelling and water density
analysis", Biophys.J., 87, 4316-25.
41) Matias,
PM, Pereira, IAC, Soares,
CM,
42) Kirichenko,
AV, Pfitzner, U,
Ludwig, B, Soares, CM, Vygodina,
TV, Konstantinov, AA (2005) “Cytochrome
c oxidase as a calcium binding protein.
Studies on
the role of a conserved aspartate in helice XI-XII cytoplasmic
loop in
cation binding.”,
Biochemistry, 44, 12391-12401.
43) Rivas, L, Soares,
CM, Baptista, AM, Simaan,
J, Di Paolo, R, Murgida,
DH, Hildebrandt, P (2005) “Electric-field induced redox
potential shifts of tetraheme cytochromes
c3 immobilised
on self-assembled monolayers studied by
surface
enhanced resonance Raman spectroscopy and simulation studies”, Biophys.J., 88,
4188-4199.
44)
45) Teixeira,
VH,
46) Oliveira, ASF, Teixeira, VH, Baptista,
AM, Soares, CM (2005)
“Reorganization and conformational
changes in the reduction of tetrahaem cytochromes.”, Biophys. J., 89, 3919-3930.
47) Valente,
FM, Oliveira, ASF, Gnadt,
N, Xavier, AV, Teixeira, M, Soares,
CM,
48) Lopes, SDN, Soares,
CM, Baptista, AM, Goormaghtigh,
E, Costa Cabral, BJ, Castanho,
MARB (2006) “Lipidic membrane induced
conformational
and orientational guidance of the
analgesic dipeptide kyothorphin.
Putative correlation towards receptor docking”, J.Phys.Chem.B, 110,
3385-3394.
49)
Franco, IS, Mota, LJ, Soares,
CM, Sá-Nogueira, I (2006) “Funtional
domains of the Bacillus subtilis
transcription factor
AraR and identification of amino acids
important for
nucleoprotein complex assembly and effector-binding”.
J.Bact., 188, 3024-3036
50) Teixeira,
VH, Baptista, AM, Soares,
CM (2006) “Pathways of H2 towards
the active site of [NiFE]-hydrogenase”,
Biophys.J., 91, 2035-45.
51)
52) Rocha, R, Leal,
SS, Teixeira, VH, Regalla,
M, Huber, H, Baptista, AM, Soares,
CM, Gomes, CM (2006) "Natural domain design: enhanced thermal stability
of
a zinc-lacking ferredoxin isoform
shows that a hydrophobic core efficiently replaces the structural metal
site”, Biochemistry, 45, 10376-10384
53) Roxo-Rosa,M,
Xu,
Z, M, Schmidt, Neto, MF, Cai,
Z, Soares, CM, D, Sheppard, DN, Amaral, MD (2006) “Revertant
mutants G550E and 4RK rescue cystic fibrosis mutants in the first
nucleotide-binding
domain of CFTR by different mechanisms”, PNAS,
103, 17891-17896
54) Iley,
J, Moreira,
R, Martins, L, Guedes, RC, Soares,
CM (2006) “The Bsmoc group as a novel
scaffold for
the design of irreversible inhibitors of cysteine
proteases” Bioorg. Med. Chem. Lett.,
16, 2738-2741
55) Araújo,
R, Silva, C, O´Neill,
A, Micaelo, N, Guebitz,
G, Soares, CM, Casal,
M, Cavaco-Paulo, A (2007) “Tailoring cutinase
activity towards polyethylene terephthalate
and
polyamide 6.6 fibers”, J. Biotechnol.,
128,
849-857.
56) Micaelo,
N, Soares, CM (2007) “
Hydration mechanisms of enzymes in nonpolar
and polar organic solvents”, FEBS J.,
274, 2424-2436.
57) Fernandes,
AT, Soares, CM,
58) Franco, I, Mota, LJ, Soares,
CM, Sá-Nogueira, I (2007) “Probing key DNA
contacts in AraR-mediated transcriptional
repression of the Bacillus subtilis arabinose regulon”,
Nucleic Acids
Res., 35, 4755-4766
59) Broco, M, Soares,
CM, Oliveira, S, Mayhew, SG, Rodrigues-Pousada,
C
(2007) “Molecular determinants for FMN-binding in Desulfovibrio gigas
Flavoredoxin”,
FEBS Lett.,
581, 4397-4402
60) Teixeira,
VH, Soares, CM, Baptista,
AM (2007) “Proton Pathways in a [NiFe]-Hydrogenase: A Theoretical
Study", Proteins, accepted
61) Gaspar,
P, Neves, AR, Shearman,
CA, Gasson, MJ, Baptista,
AM, Turner, DL, Soares, CM, Santos,
H (2007)
"The lactate dehydrogenases encoded by the
ldh and ldhB genes in Lactococcus lactis
exhibit
distinct regulation and catalytic properties: comparative modelling to
probe
the molecular basis.”, FEBS J. 274,
5924-5936
62) Rodrigues,
JV, Victor, BL, Huber, H, Saraiva,
LM, Soares, CM,
63)
64)
65) Durão,
P, Chen, Z, Silva, CS, Soares,
CM, Pereira, MM, Todorovic, S,
Hildebrandt, P, Bento,
I, Lindley, PF, Martins, LO (2008) “Proximal mutations at the type 1
copper
site of CotA-laccase; spectroscopic, redox, kinetic and structural characterization
of Ile494A
and L386A mutants”., Biochemical J.
accepted