CurriculumVitae
Cláudio M. Soares
(Simplified version)
20171127
2-Academic degrees
3-Scientific interests
4-Positions
5-Administrative activities
6-Teaching activities
7-Financed research projects
8-Work as referee
9-Participation in evaluation of
research and training projects
10- Organisation of meetings and
courses
11-Publications in peer-reviewed
journals
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
2780-157 Oeiras
Portugal
Telephone: +351 21 4469610
Fax: +351 21 441 1277
Email:
claudio@itqb.unl.pt
WWW:
http://www.itqb.unl.pt/~claudio
2-Academic degrees
- 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.
3-Scientific interests
Main
areas
Molecular modelling of biomolecules /
Structural bioinformatics, Structural Biology, Biophysics, Bioenergetics.
Specialised
areas
Redox proteins and processes, Electron
and Proton transfer, Protein structure prediction, Enzyme catalysis, Proteins
with biomedical interest, Software development for molecular modelling.
4-Positions (in reverse order)
- July 2014 to present day – Dean of
the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.
- January 2015 to the present day -
Head of the Molecular, Structural and Cellular Microbiology – MOSTMICRO
Research Unit of ITQB.
- 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:
-Ana
Sofia Oliveira, Pos-Doc
-Diana
Lousa, Pos-Doc
-João
Damas, PhD student
-Davide
Cruz, PhD student
-Barbara
Abreu, PhD student
-Cesar Pimenta, PhD student
-Tiago Barbosa, Master student
-André Marques, Master student
-Tiago
Resende, Co-supervised PhD student with Isabel Rocha, U. Minho
-Joana Azevedo Oliveira, Co-supervised
PhD student with Isabel Rocha, U. Minho
-Francisco
Fernandes, Co-supervised Pos-Doc with Alfredo Ferreira, IST, ULisboa
Former members include:
-Carla
Baltazar, former PhD student
-Daniel
Machado, Former Pos-Doc student, co-supervised with Isabel Rocha, U. Minho
-Selin Pars,
former Erasmus student from Turkey
-Andreia
Rogério, Summer student from IST-UL
-Jorge Antunes,
former Master Student
-Hélia Jeremias,
former research student, now a research student in FCUL.
-Ana Carolina
Leote, Summer student from IST-UL
-Emanuel
Lopes, Summer student from IST-UL
-Luis Demmelhuber,
former Erasmus student from University of Applied Science
Weihenstephan-Triesdorf, Germany.
-Rita Melo, former
Post-Doc, now a Post-doc in ITN
-Carlos Fernández
Rodríguez, former Erasmus student from Univ. of Leon,
Spain.
-Bruno
Victor, Post-Doc, former Post-Doc, now working in BIOSIM2 in Cantanhede,
Portugal.
-Maria Luísa
Rodrigues, former Post-Doc (also affiliated with the Computational Genomics
group, IGC, PT, headed by José Pereira Leal), now a teacher.
-Joana
Vaz, former research student, now a Master student in the UK.
-Luis
Pereira, former research student, now a research student at ITQB.
-Nuno Micaêlo,
former PhD student, now Auxiliary researcher at Universidade do Minho
-Carlos A.
Cunha,former Post-Doc, now working at DHL
-Zélia Ferreira,
Research student, now a research student at Universidade do Porto.
-Vitor Hugo
Teixeira, former PhD student, now a post-doc at Universidade do Algarve.
-Paulo J. Martel,
PhD, Assistant Prof. at Universidade do Algarve
-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, Dortmund, Germany
-Nuno Elias, BSc,
former Diploma student, now a Wine Engineer
- Member of the Scientific Council of
TAGUSPARK – Parque de Ciência e Tecnologia, Portugal. From May 2013 to the
present day.
- Member of the FEBS (Federation of
European Biochemical Societies) Advanced Courses Committee. From January 2015
to the present day.
- General Secretary of the General
Assembly of the Portuguese Biophysical Society – November 2008 to the present
day.
- President of the General Assembly of
the Portuguese Biochemical Society – January 2017 to the present day.
- Member of European Science Foundation
(ESF) College of Expert Reviewers – October
2016-October 2019
- Member of the Council of the
International Union for Pure and Applied Biophysics (IUPAB). From November 2011
to July 2017.
- General Secretary of the General
Assembly of the Portuguese Biochemical Society – January 2013 to December 2016.
- March 2013 to June 2014 – Interim
Dean of the Instituto de Tecnologia Química e Biológica, Universidade Nova de
Lisboa.
- March 2011 to March 2013 – Vice-Dean
of the Instituto de Tecnologia Química e Biológica, Universidade Nova de
Lisboa.
- May 2009 to Februry 2011 - Head of
the Biological Chemistry Division, Instituto de Tecnologia Química e Biológica,
Universidade Nova de Lisboa (mandate suspended in March 2010 when became Vice-Dean).
- December 2002 to October 2008 -
Chairman of the Portuguese Biophysical Society.
- June 2005 to February 2008 –
Vice-Dean of the Instituto de Tecnologia Química e Biológica, Universidade Nova
de Lisboa.
- Member of the Scientific Advisory
Council of the Instituto de Tecnologia Química e Biológica, Universidade Nova
de Lisboa - 2003 until 2008.
- Member of the Co-ordinating Committee
of the Scientific Council of the Instituto de Tecnologia Química e Biológica,
Universidade Nova de Lisboa - 1999 until the end of 2002.
- February 1999 until February 2005 -
Invited Assistant Professor at the Instituto de Tecnologia Química e Biológica,
Universidade Nova de Lisboa.
- November 1998 to January 1999 -
Research associated at the Instituto de Tecnologia Química e Biológica, Universidade
Nova de Lisboa. Co-ordinator of the Protein Modelling Unit.
- November 1994 to October 1998 -
Post-doc at the Instituto de Tecnologia Química e Biológica, Universidade Nova
de Lisboa, in the group of Prof. Maria A. Carrondo. During this time he was
responsible for the co-ordination of the Protein Modelling Unit formed
meanwhile.
- November 1990 to April 1993 - PhD
student with a JNICT scholarship at the Department of Physical Chemistry,
Uppsala University, Sweden, under the supervision of Professor Orlando Tapia.
- October 1988 to September 1989 -
Diploma student at the Centro de Bioquímica e Fisiologia Animal do Instituto
Rocha Cabral, Lisbon under the supervision of Prof. Ana Ponces Freire.
5-Administrative activities
Dean of the Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa - July 2014 to
present day.
Interim Dean of the Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa - March 2013 to June
2014.
Vice-Dean of the Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa - March 2011 to March
2013.
Member
of the Scientific Council of ITQB –From 2009 to February 2011
(mandate suspended in March 2010 when became Vice-Director).
Member
of the Pedagogical Council of ITQB –From 2009 to February 2011
(mandate suspended in March 2010 when became Vice-Director).
Member
of the Institute Council of ITQB –From 2009 to February 2011
(mandate suspended in March 2010 when became Vice-Director).
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 to October 2008.
Member
of the directing board of the Portuguese Biophysical Society.
From 1998 to the end of 2002. From
November 2008 to the present day.
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.
6-Teaching activities
Supervision
of Pos-Docs: Responsible for the supervision of 8
pos-doctoral fellows.
Supervision
of PhD students: Responsible for 7 PhD students that
have finished and 6 PhD students currently doing their research.
Supervision
of Diploma students: Responsible for 5 Diploma students
that have finished.
Supervision
of Master (pos-Bologna) students: Responsible for 2 Master
students that has finished and 2 students pursuing the degree.
Supervision
of Research students: Responsible for 14 research students,
8 of which have become PhD students meanwhile.
Teaching
activities in PhD programs: Biomolecular modelling techniques in several
ITQB-UNL PhD program (in the years of 1999, 2003-2017). 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
7-Financed research projects
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
xvii) Responsible for the protein
modelling activities in the FCT project PTDC/BIO/73946/2006. “Site-specific
labeling of proteins by a novel type of transglutaminase isolated from spores
of Bacillus subtilis.”. 2009-2012
xviii) Responsible for the protein
modelling activities in the FCT project PTDC/QUI/65640/2006 “Investigation of
redox-state-specific protein-protein interactions and energy transduction in
the electron transfer chains of sulfate reducing bacteria”. 2009-2011
xix) Responsible for the protein
modelling activities in the MIT-Pt/BS-BB/0014/2008 project “Structural and
functional study of the proteins mediating electron transfer between
microorganisms and solid substrates with relevance for bio-energy production”.
2009-2012
xx) Responsible for the protein
modelling activities in the FCT PTDC/AGR-AAM/102345/2008 project “Breaking Down The Wall - Microbial Hemicellulases for
saccharification”. 2010-2012
xxi) Involved in the FCT project
PTDC/QUI-BIQ/105238/2008 “Study of pH-dependent protein misfolding using
state-of-the-art molecular modelling methods”. 2010-2012.
xxii) Involved in the FCT project
PTDC/BIA-PRO/104378/2008 “Including protonation effects in the simulation of
peptides and proteins in membrane environments”. 2010-2012
xxiii) Principal researcher in the FCT
project PTDC/QUI-BIQ/113446/2009 entitled "Proton transfer and proton
pumping in haem-copper oxidases. Methodological developments
and their application to unravel the molecular mechanism ". 2010-
2014.
xxiv) Principal researcher in the FCT project PTDC/QUI-BIQ/114774/2009 entitled "Membrane fusion mechanism of Influenza Hemagglutinin: a simulation and biophysical approach." 2010- 2014.
xxv) Responsible for the protein modelling activities in the PTDC/QUI-BIQ/117799/2010 entitled “Interaction of proteins with CO releasing molecules (CORMS).” 2011-2014.
xxvi) Responsible for the protein modelling
activities in the PTDC/BBB-BEP/0934/2012 entitled “Structural Determinants of
Oxygen Tolerance in a NiFeSe Hydrogenase.” 2013-2014.
xxvii) Responsible for the protein
modelling activities in the PTDC/BBB-BEP/2885/2014 entitled “Engineering a
highly active NiFeSe Hydrogenase for electrocatalytic and photocatalytic
applications.” 2016-2018.
xxviii) Principal researcher in the European PRACE Preparatory Access Proposal 2010PA3220 entitled “Probing the pH-induced conformational change of influenz hamaggglutinin using micro-second long simulations“.– 205.000 Core-hours. 2016
8-Work as referee and
editor in scientific journals
As member of the Editorial Board
i) Biophysical Reviews – In the years
of 2011-2017.
ii) PLOS One – In the years of
2012-2017.
iii) Scientific Reports – In the year
of 2013-2017
As associate editor.
i) Journal of Biophysics – In the years
of 2008-2018. Terminated.
ii) BioMed Research International (old
Journal of Biomedicine and Biotechnology) – In the years of 2008-2017
As referee
i) Biopolymers - In the year of 1999.
ii) Proteins - In the years of 2000 and
2004.
iii) Biophysical Journal - In the years
of 2002, 2006, 2010, 2011, 2015, 2016 and 2017.
iv) Journal
of Biological Inorganic Chemistry- In the years of 2002, 2003, 2009 and 2013.
v) Protein Science - In the years of
2003, 2004 and 2010.
vi) Journal
of Computational Chemistry - In the year of 2003.
vii) FEBS Letters – In the years of
2005, 2006, 2011, 2013, 2015.
viii) Journal of Cystic Fibrosis - In
the year of 2004.
ix) Protein Engineering Design and
Selection – In the years of 2005 and 2012.
x) Biophysics (Biophysical Society of
Japan) – In the year of 2006
xi) Journal of Chemical Physics – In
the years of 2006, 2008, 2013, 2015 and 2017
xii) Journal of Biotechnology – In the
year of 2006
xiii) Journal of Physical Chemistry –
In the years of 2006, 2007, 2008, 2010, 2011, 2014, 2015, 2016.
xiv) BMC Biotechnology – In the year of
2006
xv) Journal of Molecular Graphics and
Modelling – In the years of 2006, 2009, 2012 and 2013.
xvi) Chemical Physics Letters – In the
years of 2006, 2012, 2014
xvii) Extremophiles – In the years of
2007, 2008 and 2010
xviii) Journal of Computer-Aided
Molecular Design – In the years of 2007 and 2010.
xix) Molecular Simulation – In the
years of 2008 and 2013.
xx) Journal of Molecular Catalysis – In
the years of 2008 and 2012.
xxi) Protein and Peptide Letters – In
the years of 2008 and 2012.
xxii) FEBS Journal – In the year of
2008
xxiii) Journal of Peptide Science – In
the year of 2007
xxiv) Process Biochemistry – In the
year of 2009
xxv) International Journal of Molecular
Sciences – In the year of 2010
xxvi) Langmuir – In the years of 2010
and 2016
xxvii) Journal of the American Chemical
Society – In the years of 2010 and 2011.
xxix) Biotechnology and Bioengineering
– In the years of 2011 and 2016
xxx) Journal of Chemical Information
and Modeling – In the year of 2011.
xxxi) Theoretical Chemistry Accounts –
In the year of 2012.
xxxi)
Proc. Natl. Acad. Sci. USA – In the year of 2011.
xxxii) The Protein Journal – In the
year of 2011.
xxxiii) Journal of Chemical Information
and Modelling – In the year of 2011.
xxxiv) Bioresource Technology – In the
year of 2011.
xxxv) PLOS One – In the years of 2011
and 2012.
xxxvi) Journal of Molecular Modelling –
In the year of 2011.
xxxvii) ChemPhysChem – In the year of
2012.
xxxviii) FEMS Microbiology Letters – In
the year of 2012.
xxxix) ACS Chemical Biology – In the
year of 2012.
xxxx)
International Journal of Biological Macromolecules – In the year of 2013
xxxxi)
Advances in Biology – In the year of 2013
xxxxii)
BBA-Biomembranes – In the year of 2014
xxxxiii)
Biochemistry – In the years of 2014 and 2016
xxxxiv)
Journal of Chemical Theory and Computation – In the years of 2014 and 2016
xxxxv)
PLOS Computational Biology – In the year of 2014
xxxxvi)
Journal of Physical Chemistry Letters – In the year of 2015
xxxxvii)
Physical Chemistry Chemical Physics – In the year of 2015
xxxxviii)
Enzyme and Microbial Technology – In the year of 2015
xxxxix)
PeerJ – In the year of 2016
xxxxx)
Molecular Physics – In the year of 2016
xxxxxi)
International Journal of Molecular Sciences – In the year of 2017
9- Participation in evaluation of research
and training projects, and prizes
i) Evaluation of Marie Curie Research
Training Networks, both remotely as well as in Brussels, Belgium, during the
FP6-2002-Mobility-1 call - end of February, beginning of March, 2004.
ii) Evaluation of FP6-NEST research
projects, in the 2003 call, at the end of May 2004.
iii) Evaluation of Marie Curie Research
Training Networks, both remotely as well as in Brussels, Belgium, during the
FP6-2004-Mobility-1 call – end of February, beginning of March, 2005.
iv) Evaluation
of Marie Curie fellowships, both remotely as well as in Brussels, Belgium,
during the FP6-Mobility-5/6/7 LIF call – April and May, 2006.
v) Evaluation of projects PICT from the
Agencia Nacional de Promoción Cientifíca y Tecnológicas (Argentina). 2007, 2008, 2010 and 2011.
vi) Evaluation
of a project from the Grant Agency, Academy of Sciences of the Czech Republic.
2008.
vii) Evaluation of Marie Curie
fellowships both remotely as well as in Brussels, Belgium, during the
FP7-PEOPLE-IEF/IOF/IIF-2008 LIF call – October 2008.
viii) Evaluation of a project from the
NWO Grant Agency of The Netherlands. 2009.
xix) Evaluation of Marie Curie
fellowships, both remotely as well as in Brussels, Belgium, during the
FP7-PEOPLE-2009-IEF-IIF-IOF LIF call – October, 2009.
xx) Speaker in the information session
“Acções Marie Curie” held at ITQB where he presented a talk entitled “The
experience of a Marie Curie Evaluator”. May 17th, 2010.
xxi) Evaluation of Marie Curie
fellowships, both remotely as well as in Brussels, Belgium, during the
FP7-PEOPLE-2010-IEF-IIF-IOF LIF call – October, 2010.
xxii) Evaluation of a project from the
National Science Foundation, USA, 2011.
xxiii) Evaluation of Marie Curie Career
Integration Grants, both remotely as well as in Brussels, Belgium, during the
FP7-PEOPLE-2011-CIG call – April, 2011.
xxiv) Evaluation of a project from the
Emmy Noether-Programm Nachwuchsgrupper Neuantrag of the German Research
Foundation (Deutsche Forschungsgemeinschaft), Germany, 2011.
xxv) Evaluation of two projects for the
Austrian Science Fund, Austria, 2011.
xxv) Evaluation of two research
projects for the Cyprus Research Promotion Foundation, Cyprus, 2011.
xxvi) Evaluation of a research proposal
from Agência de Inovação, Portugal. 2011.
xxvii) Evaluation of Marie Curie
fellowships, both remotely as well as in Brussels, Belgium, during the
FP7-PEOPLE-2011-IEF-IIF-IOF LIF call – October, 2011.
xxviii) Evaluation of Marie Curie
Career Integration Grants, both remotely as well as in Brussels, Belgium,
during the FP7-PEOPLE-2012-CIG call – April, 2012.
xxvix)
Evaluation of two projects from the National Science Centre, Poland, 2012
xxx)
Evaluation of National Fundação para a Ciência e Tecnologia PhD and
Post-Doctoral fellowships in the Biological Sciences Panel – July 2012.
xxxi) Evaluation of a project from the
American Chemical Society Petroleum Research Fund – July 2012.
xxxii) Evaluation of a project from the
Romanian National Research Council – August 2012.
xxvii) Evaluation of Marie Curie
fellowships, both remotely as well as in Brussels, Belgium, during the
FP7-PEOPLE-2012-IEF-IIF-IOF LIF call – October, 2012.
xxxiii)
Member of the jury of the Santander Totta – Universidade Nova de Lisboa award,
2012/2013 Edition – Exact Sciences and Engeneering. January-Februry
2013.
xxxiii) Speaker in the information
session “FP7 / Marie Curie / Sessão de Informação Bolsas Individuais” held at
Reitoria da Universidade de Lisboa where he presented a talk entitled
“Evaluating Individual fellowships: an experience”. March 14th, 2013.
xxxiv) Evaluation of one project from
the National Science Centre, Poland, 2013.
xxxv) Evaluation of one projects for
the Austrian Science Fund, Austria, 2013.
xxxvi) Evaluation of FP7 ERA Chairs,
both remotely as well as in Brussels, Belgium, during the– July, 2013.
xxxvii) Evaluation of Marie Curie fellowships, both remotely as well as in Brussels, Belgium, during the FP7-PEOPLE-2013-IEF-IIF-IOF LIF call – October, 2013.
xxxviii) Speaker in the information session “What’s in Horizon2020 for me?” held at Faculdade de Medicina da Universidade de Lisboa where he presented a talk entitled “Marie Skłodowska-Curie individual fellowships: a perspective from an evaluator’s side”. December 20th, 2013.
xxxix) Evaluation of Marie Curie fellowships, both remotely as well as in
Brussels, Belgium, during the H2020-MSCA-IF-2015 call – November, 2015. During
this period he has evaluated 23 proposals, being the rappourteur of 8.
xxxx) Evaluation of one project from the United States-Israel Binational
Science Foundation, Israel, 2016.
xxxxi) Chair of the Experimental Biology
and Biochemistry panel for the national evaluation of PhD and Post-Doctoral
Fellowships from Fundação para a Ciência e Tecnologia (National Science
Foundation, Portugal), 2016-2017
xxxxii) Evaluation of one project from the National Science Centre,
Poland, 2016.
xxxxiii) Evaluation of two projects from the National Science Centre,
Poland, 2017.
xxxxiv) Evaluation of one project from the Deutsche Forschungsgemeinschaft
(German Research Foundation) on the Emmy Noether Programme, Germany, 2017.
xxxxv) Evaluation one individual proposal (36 months) from the Deutsche Forschungsgemeinschaft (German Research Foundation), Germany, 2017
11-Organisation
of meetings and courses
i) Main organiser of the 2nd Short course
of the Portuguese Biophysical Society "Simulation of biological processes.
Practical approaches" – 2-3 of October 1999,
ii) In the organisation of the 3rd
Short course of the Portuguese Biophysical Society "Proteins: from
structure to dynamics" – 4-6 of October 2001,
iii) In the organisation of the 4th
Short course of the Portuguese Biophysical Society "Bioenergetics: the
cellular power plants" - 5-6 of October 2002,
iv) In the
organisation of the 5th Short course of the Portuguese Biophysical Society
"Genomics and Proteomics: biophysical perspectives". 17-19 of October 2003,
v) Main organiser of the 3rd
Portuguese-Spanish Biophysics Congress. 29th October until
November 1st 2004 in
vi) In the
organisation of the 6th Short course of the Portuguese Biophysical Society
"From cellular transport to neurosciences: a biophysical
perspective". 14-16 of October 2005,
vii) In the organisation of the 8th
European Biological Chemistry Conference, EUROBIC 8. 2-6 of
July, 2006,
viii) In the organisation of the
Oxizymes in Oeiras: 3rd European Meeting in Oxizymes, September 7-9, 2006,
ix) In the organising and scientific
committees of the VI Ibero-American Congress of Biophysics, September 24-27,
2006,
x) In the organisation of the 7th Short
course of the Portuguese Biophysical Society "Biospectroscopy and
Imaging". 19-21 of October 2007,
xi) Main organiser of the 1st
Portuguese-Spanish-British Joint Biophysics Congress 2008, 10-13th July, 2008,
Lisbon, Portugal
xii) In the organisation of the
Workshop “Structure, dynamics, and function of proteins”, 17-19 September,
2008, ITQB-UNL,
xiii) In the organisation of the 8th
Short course of the Short course of the Portuguese Biophysical Society
"Systems Biology". 30 October - 1 November 2009,
xiv) In the Scientific Committee of the
IV Spanish-Portuguese Biophysical Congress. 7-10 July 2010,
xv) In the Scientific Committee of the
Xth Spanish Symposium on Bioinformatics (JBI2010), 27-29 October,
xvi) In the organisation of the 9th
Short course of the Short course of the Portuguese Biophysical Society
"Protein folding, misfolding and disease". 8-10
October 2010,
xvii) In the Scientifc Committee of the
Congresso Nacional de Bioquímica 2010, 15-17 December 2010,
xviii) In the organisation of the 10th
Short course of the Short course of the Portuguese Biophysical Society
"Nanosciences for Life". 17-19 November 2011,
xix) In the organising committee of the
“Jornadas de Bioinformática” 2012. 23-25 January 2012,
xxi) In the organisation of the EBSA
(European Biophysical Societies' Association) 2013, Lisbon, Portugal
xxii) In the Scientific Committee of
the XIX National Congress of Biochemistry, 8-10 December, 2016, Guimarães,
Portugal.
xxiii) In the organisation of the 5th
Iberian Biophysics Congress EBSA 15-17 June, 2016, Porto, Portugal
xxiv) In the National Organising
Committee of the XXV National Meeting of the Portuguese Chemical Society, 16-19
of July of 2017, Lisbon, Portugal
xxv) In the Scientific Committee of the
19th IUPAB congress and 11th EBSA congress, Edinburgh,Scotland, UK, 16-20 July,
2017
10-Publications in ISI peer-reviewed journals
Co-author of 107 published or accepted
papers in scientific journals. Co-author of 3 submitted manuscripts. Co-author of 2 papers in peer-reviewed book chapters. Co-author of 1 paper in a submitted peer-reviewed book chapter.
Author of a review in a Portuguese publication.
ResearcherID: E-2675-2012
At 2017-11-27
Total number of accessible articles: 107
Total number of citations: 3494
Average citations per article: 32.65
h-index: 35
http://orcid.org/0000-0003-1154-556X
Scopus Author ID: 34973451500
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
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) Mendes, J, Nagarajaram, HA, Soares, CM,
Blundell, TL,
24) Mendes, J, Baptista, AM,
25)
26) 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
27) Teixeira, VH, Soares, CM, Baptista, AM
(2002) "Studies of the reduction and protonation behaviour of tetrahaem
cytochromes using atomic detail", JBIC,
7, 200-216
28) Martins, LO, Soares, CM,
29) Baptista, AM, Teixeira, VH, Soares, CM
(2002) "Constant-pH molecular dynamics using stochastic titration", J.Chem.Phys., 117, 4184-4200
30) 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
31) 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
32) Bento, I, Teixeira, VH, Baptista, AM, Soares,
CM, Matias, PM,
33)
34) 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
35) 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
36) Soares, CM, Baptista, AM,
37) Teixeira, VH, Baptista, AM, Soares, CM
(2004) “Modelling electron transfer thermodynamics in protein complexes:
interaction between two cytochromes c3", Biophys.J., 86, 2773-2785
38) 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
39) Victor, BL, Baptista, AM, Soares, CM
(2004) "Theoretical identification of proton channels in the Quinol
Oxidase aa3 from Acidianus ambivalens", Biophys.J., 87, 4316-25.
40) Matias, PM, Pereira, IAC, Soares, CM,
41) 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.
42) 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.
43)
44) Teixeira, VH,
45) Oliveira, ASF, Teixeira, VH, Baptista, AM, Soares,
CM (2005) “Reorganization and conformational changes in the reduction of
tetrahaem cytochromes.”, Biophys. J., 89,
3919-3930.
46) Valente, FM, Oliveira, ASF, Gnadt, N, Xavier,
AV, Teixeira, M, Soares, CM, Pereira, IAC (2005) “Hydrogenases in
Desulfovibrio vulgaris Hildenborough: structural and physiologic
characterisation of the membrane-bound [NiFeSe] hydrogenase”, JBIC, 10, 667-682.
47) Lopes, SDN, Soares, CM, Baptista, AM,
Goormaghtigh, E, Costa Cabral, BJ, Castanho, MARB (2006) “Conformational and
orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic
membranes: Putative correlation toward receptor docking”, J.Phys.Chem.B, 110,
3385-3394.
48) 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
49) Teixeira, VH, Baptista, AM, Soares, CM
(2006) “Pathways of H2 towards the active site of
[NiFE]-hydrogenase”, Biophys.J.,
91, 2035-45.
50)
51) 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
52) 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
53) 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
54) 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.
55) Micaelo, N, Soares, CM (2007) “Modeling
hydration mechanisms of enzymes in nonpolar and polar organic solvents”, FEBS J., 274, 2424-2436.
56) Fernandes, AT, Soares, CM,
57) 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
58) 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
59) 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
60) Teixeira, VH, Soares, CM, Baptista, AM (2008)
“Proton Pathways in a [NiFe]-Hydrogenase: A Theoretical Study", Proteins, 70, 1010-1022
61) Rodrigues, JV, Victor, BL, Huber, H, Saraiva,
LM, Soares, CM,
62)
63)
64) 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. 412, 339-346
65) Escrevente, C,
66) Fonseca, BM, Saraiva, IH, Paquete, CM, Soares, CM, Pacheco, I, Salgueiro, CA, Louro, RO (2009) “The tetrahaem cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the different haems”, JBIC, 14, 375-385
67) Victor, BL, Baptista, AM, Soares, CM (2009) “Dioxygen and nitric oxide pathways and affinity to the catalytic site of ROO from Desulfovibrio gigas”, JBIC, 14, 853-862
68) Gonçalves, S, Borges, N, Esteves, AM, Victor, B, Soares, CM, Santos, H, Matias, PM (2010) “Structural Analysis of Thermus thermophilus HB27 Mannosyl-3-phosphoglycerate Synthase Provides Evidence for a Second Catalytic Metal Ion and New Insight into the Retaining Mechanism of Glycosyltransferases “, J Biol Chem, 285, 17857-17868
69) Oliveira, ASF, Baptista, AM, Soares, CM (2010) “Insights into the ATP-hydrolysis mechanism of an ABC-transporter: conformational changes in the NBD dimer of MJ0796”, J Phys Chem B, 114, 5486-5496
70)
Fernandes, AT, Damas, JM, Todorovic, S, Huber, R, Pogni, R, Soares, CM,
Martins, LO (2010) “The Multicopper Oxidase from the Archaeon Pyrobaculum
aerophilum Shows Nitrous Oxide Reductase Activity”, FEBS J., 277, 3176-3189
71) Bento, I, Silva, C, Chen, Z, Martins, LO, Lindley, PF, Soares, CM (2010) “Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies.”, BMC Struct. Biol. 2010, 10:28.
72) Machuqueiro, M,
73) Lousa, D, Baptista, AM, Soares, CM (2011) “Structural determinants of ligand imprinting: a molecular dynamics simulation study of subtilisin in aqueous and apolar solvents”, Prot.Sci., 20, 379-86.
74) Baltazar, C, Marques, MC, Soares, CM, DeLacey, AM,
75) Oliveira, ASF, Baptista, AM, Soares, CM (2011) “Conformational changes induced by ATP-hydrolysis in an ABC transporter: a molecular dynamics study of the Sav1866 exporter”, Proteins, 79, 1977-1990
76) Damas, JM, Oliveira, ASF, Baptista, AM, Soares, CM (2011) “Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: molecular dynamics studies of HlyB”, Prot.Sci., 20, 1220-1230
77) Varanda, C, Felix, MR, Soares, CM, Oliveira, S, Clara, MI (2011) “Specific amino acids of Olive mild mosaic virus coat protein are involved on transmission by Olpidium brassicae”, J. Gen.Virol., 92, 2209-2213
78) Oliveira, ASF, Baptista, AM, Soares, CM (2011) “Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex”, PLoS Comp.Biol., 7(8), e1002128
79) Soares, CM, Baptista, AM (2012) “Simulation of multihaem cytochromes”, FEBS Lett., 586, 510-518 (joint corresponding author).
80) Silva, CS, Damas, JM, Chen, Z., Brissos, V, Martins, LO, Soares, CM, Lindley, PF, Bento, I (2012) “The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase: assistance during the proton transfer mechanism”, Acta Crys D, D68,186-193. (joint corresponding author).
81) Azoia, NG, Fernandes, MM,
82) Baltazar, CSA, Teixeira, VH, Soares, CM (2012) “Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach”, JBIC, 17, 543-555
83) Lousa, D, Baptista, AM, Soares, CM (2012) “Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations”, J.Chem.Infor.Model., 52: 465-473
84) Lousa, D, Cianci, M, Helliwell, JR, Halling, PJ, Baptista, AM, Soares, CM (2012) “Interaction of counterions with subtilisin in acetonitrile: Insights from molecular dynamics simulations”, J.Phys.Chem.B, 116, 5838–5848
85)
86) Pires, S, Sezer, M, Soares, CM, Hemmingsen, L, Iranzo, O (2012) “Design of a peptidic turn with high affinity for Hg(II)”, Inorg.Chem., 51, 11339–11348.
87) Victor, BL, Baptista, AM, Soares, CM (2012) “Structural determinants for the membrane insertion of the transmembrane peptide of hemagglutinin from Influenza virus”, J.Chem. Infor. Model., 52, 3001–3012
88) Fonseca, BM, Paquete, CM, Neto, SE, Pacheco, I, Soares, CM, Louro, RO (2013) “Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1”, Biochem. J., 449, 101-8.
89) Gutiérrez-Sanz, O, Marques, MC, Baltazar, CSA, Fernández, VM, Soares,
CM,
90) Volkers, G, Damas, JM, Palm, GJ, Panjikar, S, Soares, CM, Hinrichs, W (2013) “Putative dioxygen binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX”, Acta Crys, D69, 1758-1767.
91) Lousa, D, Baptista, AM, Soares, CM (2013) “A molecular
perspective on nonaqueous biocatalysis: Contributions from simulation studies” Phys.Chem.Chem.Phys.,
15, 13723-13736
91) Lousa, D, Baptista, AM, Soares,
CM (2013) “A molecular perspective on nonaqueous biocatalysis: Contributions
from simulation studies” Phys.Chem.Chem.Phys.,
15, 13723-13736
92) Damas, JM, Filipe, LCS, Campos, SRR, Lousa, D, Victor, BL, Baptista, AM,
Soares, CM (2013) “Predicting the thermodynamics and kinetics of helix
formation in a cyclic peptide model”, J.Chem.Theor.Comp.,
9, 5148-5157
93) McVey, CE, Ferreira, MJ, Correia, B,
Lahiri, S, de Sanctis, D, Carrondo, MA, Lindley, PF, de-Sá-Nogueira, I, Soares,
CM, Bento, I (2014) “The importance of the Abn2 calcium cluster in the
endo-1,5-arabinanase activity from Bacillus
subtilis”, JBIC, 19, 505-513. (joint corresponding
author)
94) Damas, JM, Baptista, AM, Soares,
CM (2014) “A New Pathway for O2 Diffusion inside CotA Laccase and Implications
on the Multicopper Oxidases Family”, JCTC,
10, 3525–3531
95) Paquete, CM, Fonseca, BM, Cruz, DR,
Pereira, T, Pacheco, I, Soares, CM, Louro, RO (2014) Molecular
mechanisms of electron shuttling across the microbe/metal space: Exploring the
final frontier”, Frontiers in
Microbiology, 5, 318.
96) Oliveira, ASF, Damas, JM, Baptista, AM,
Soares, CM (2014) “Exploring O2 diffusion in A-type Cytochrome c
Oxidases: molecular dynamics simulations uncover two alternative channels
towards the binuclear site, PLoS
Comp.Biol., 10, e1004010
97) Nobre, LS, Lousa, D, Pacheco, I, Soares,
CM, Teixeira, M, Saraiva, LM (2015) “Insights into the structure of the diiron
site of RIC from Escherichia coli”, FEBS
Lett., 589, 426-433
98) Victor, BL, Lousa, D, Antunes, J, Soares,
CM (2015) “Self-assembly molecular dynamics simulations shed light into the
interaction of the influenza fusion peptide with a membrane bilayer”, J.Chem. Infor. Model., 55, 795–805
99) Alves, MN, Neto, SE, Alves, AS,
Carrêlo, A, Pacheco, I, Fonseca, BM, Paquete, CM, Soares, CM, Louro, RO
(2015) “Characterization of the periplasmic redox network that sustains the versatile anaerobic
metabolism of Shewanella oneidensis MR-1”, Frontiers in Microbiology, 6, 665
100) Fernandes, CG, Plácido, D, Lousa, D,
Brito, JAA, Isidro, A, Soares, CM, Pohl, J, Carrondo, MA, Archer, M,
Henriques, AO (2015) “Structural and functional characterization of an ancient
bacterial transglutaminase sheds light into the minimal requirements for
protein cross-linking”, Biochemistry,
54, 5723-5734
101) Oliveira, ASF, Campos, SRR, Baptista,
AM, Soares, CM (2016) “Coupling between protonation and conformation in
cytochrome c oxidase: Insights from Constant-pH MD simulations”, BBA Bioenergetics, 1857, 759-771.
102) Lousa, D, Pinto, ART, Victor, BL,
Laio, A, Veiga, AS, Castanho, MARB, Soares, CM (2016) “Fusing simulation
and experiment: The effect of mutations on the structure and activity of the
influenza fusion peptide”, Sci.Rep., 6,
28099.
103) Romão, CV, Vicente, JB, Borges, PT,
Victor, BL, Lamosa, P, Silva, E, Pereira, L, Bandeiras, TM, Soares, CM,
Carrondo, MA, Turner, D, Teixeira, M, Frazão, C. (2016) “Structure of Escherichia coli Flavodiiron nitric
oxide reductase”, J.Mol.Biol., 48, 4686-4707
104) Marreiros, BC,
Sena, FV, Sousa, FM, Oliveira, ASF, Soares, CM, Batista, AP, Pereira, MM
(2017) “Structural and Functional insights into the catalytic mechanism of Type
II NADH:quinone oxidoreductases family”, Sci.Rep.,
7, 42303
105) Magalhães, PR, Oliveira, ASF, Campos,
SRR, Soares, CM, Baptista, AM. (2017) “Effect of a pH gradient on the
protonation states of cytochrome c oxidase: a CE/MC study”, JCIM, 57, 256-266.
106) Pereira, L,
Saraiva, IH, Oliveira, AS, Soares, CM, Louro, RO, Frazão, C. (2017) “Molecular
structure of FoxE, the putative iron oxidase of Rhodopseudomonas ferrooxidans
SW2”, BBA Bioenergetics, 1858, 847-853
107) Sousa, FM,
Sena, FV, Batista, AP, Athayde, D, Brito, JA, Archer, M, Oliveira, ASF, Soares,
CM, Catarino, T, Pereira, MM (2017) “The key role of glutamate 172 in the
mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus”, BBA
Bioenergetics, 1858, 823-832
108) Almadanim, MC, Gonçalves, NM, Rosa, MTG, Alexandre, BM, Cordeiro, AM, Rodrigues, M, Saibo, NJM, Soares, CM, Romão, CV, Oliveira, MM, Abreu, IA (2017) “The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications”, BBA Molecular Cell Research, accepted.