Curriculum Vitae

 

Name:                                       Cláudio Manuel Simões Loureiro Nunes Soares

Place and date of birth:              Torres Vedras, Portugal, August 24th, 1966

Official address:

        ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa

        Av. da República,

        2780-157 Oeiras

        PORTUGAL

        Tel: +351 21 4469259/610

        Email: claudio@itqb.unl.pt           WWW: http://www.itqb.unl.pt/~claudio     

 

Education (degrees, dates, universities):    

   Agregação in Molecular Biosciences, 2021, ITQB NOVA, Universidade Nova de Lisboa.

   PhD in Biochemistry (theoretical), 1994, Faculdade de Ciências da Universidade de Lisboa (all the work developed in the Uppsala University).

   Filosofie Licentiatexamen, 1994, Department of Physical Chemistry, Uppsala University, Sweden.

   Licenciatura in Biochemistry, 1989, Faculdade de Ciências da Universidade de Lisboa.

 

Current positions:

    Dean of the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa - March 2013 to present day.

    Coordinator of the Molecular, Structural and Cellular Microbiology – MOSTMICRO-ITQB Research Unit of ITQB NOVA - January 2015 to the present day.

   Coordinator of the Protein Modelling Laboratory at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa - February 1999 to the present day.

   Full Professor of Biochemistry at Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa – April 2022 to the present day

   First Secretary of the General Assembly of the Portuguese Biophysical Society – November 2008 to the present day.

   President of the Scientific Council of TAGUSPARK – Parque de Ciência e Tecnologia, Portugal. From July 2020 to the present day.

 

 

Past positions:

   Associate Professor, Instituto de Tecnologia Química e Biológica – Universidade Nova de Lisboa. From March 2005 to March 2022.

   President of the Fiscal Committee of the Portuguese Biochemical Society – January 2019 to December 2022.

   Member of the Scientific Council of TAGUSPARK – Parque de Ciência e Tecnologia, Portugal. From May 2013 to June 2020.

   President of the General Assembly of the Portuguese Biochemical Society – January 2017 to December 2018.

   Member of the FEBS (Federation of European Biochemical Societies) Advanced Courses Committee. From January 2015 to December 2018.

   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.

   Vice-Dean of the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa - March 2011 to March 2013

   Head of the Biological Chemistry Division, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa- May 2009 to Februry 2011

   Member of the Scientific Council of ITQB –From May 2009 to February 201.

   Member of the Institute Council of ITQB –From May 2009 to February 2011.

   Member of the Pedagogical Council of ITQB –From May 2009 to February 2011.

   Chairman of the Portuguese Biophysical Society - December 2002 to October 2008               

   Vice-Dean of the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa - June 2005 to February 2008

   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.

   Invited Assistant Professor at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa - February 1999 until February 2005

   Research associate at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Co-ordinator of the Protein Modelling Unit - November 1998 to January 1999

   Post-doc at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. During this time he was responsible for the co-ordination of the Protein Modelling Unit formed meanwhile - November 1994 to October 1998 -

   PhD student, Department of Physical Chemistry, Uppsala University, under the supervision of Professor Orlando Tapia - November 1990 to April 1994

   Diploma student at the Centro de Bioquímica e Fisiologia Animal do Instituto Rocha Cabral, Lisbon under the supervision of Prof. Ana Ponces Freire - October 1988 to September 1989 -

 

Main areas of research:

   Molecular modelling of biomolecules / Structural bioinformatics, Structural Biology, Biophysics, Bioenergetics

Specialised areas

   Redox proteins and processes, Electron and Proton transfer, Viral fusion, Protein and Enzyme design, Proteins with biomedical interest, Software development for molecular modelling.

 

Supervision Experience

         He has supervised 5 Diploma students, 5 master students (3 have already finished the degree, 14 research students, 15 PhD students (10 have already finished the degree) and 10 post-doctoral fellows.

Present research staff of the Protein Modelling Laboratory led by CM Soares:

         -Diana Lousa, Junior Investigator

         -Davide Cruz, PhD student

         -Cesar Pimenta, PhD student

         -Mariana Valério, PhD student, Co-supervised with Diana Lousa (ITQB NOVA) and Manuel Melo (ITQB NOVA)

         -Alexandra Balola, PhD student, Co-supervised with Isabel Rocha (ITQB NOVA)

         -Pedro Moreira, PhD student, Co-supervised with Diana Lousa (ITQB NOVA) and Miguel Rocha (U. Minho)

         -Ana Carolina Buga, Master student, Supervised by Diana Lousa (ITQB NOVA) and co-supervised by Ana Salomé Veiga, iMM, FMUL

         -Susana Parreiras, Master student, Supervised by Diana Lousa (ITQB NOVA) and co-supervised by João Vicente (ITQB NOVA)

         -Fábio Queiróz, Master student, Co-supervised by Caio Souza (ITQB NOVA)

         -Rita Teixeira, Master student, Supervised by Diana Lousa (ITQB NOVA) and co-supervised by João Vicente (ITQB NOVA)

         -Bárbara Fernandes, Master student, Supervised by João Vicente (ITQB NOVA) and co-supervised by Diana Lousa (ITQB NOVA)

         -Carina Afonso, Master student, Supervised by Miguel Rocha (U.Minho) and co-supervised by Diana Lousa (ITQB NOVA)

 

 

Publications

         Co-author of 128 published or accepted papers in scientific journals. Co-author of 2 submitted manuscript. Co-author of 3 papers in peer-reviewed book chapters. Co-author of 1 paper in a submitted peer-reviewed book chapter.

 

Scopus Author ID: 34973451500

At 2023-03-25

Total citations: 5336

h-index: 40

 

Google Scholar

At 2023-03-25

Total citations: 7214

h-index: 46

 

 

ResearcherID: E-2675-2012

ResearcherID: E-2675-2012

At 2023-03-25

Total citations: 4954

h-index: 39

 

Orcid:

http://orcid.org/0000-0003-1154-556X

 

 

Seminars and invited talks in scientific meetings

         Co-author of 83 invited presentations in scientific meetings and institutions. He was the speaker in 46 of them.

 

Financed Research Projects

         He lead or participated in 36 externally financed Research Projects, from National and European Agencies.

 

Member the Editorial Boards of Scientific Journals

         i) Biophysical Reviews – From 2011-2018.

         ii) PLOS One – From 2012 to the present day.

         iii) Scientific Reports – From 2013 to the present day.

         iv) FEBS Open Bio – From 2018 to the present day.

 

Evaluation work

         He has been very active in the evaluation of research projects and prizes. Most of this evaluation work has been done for foreign agencies and for the European Commission. For some agencies I was evaluator, but in others I was member of panels. I had leadership roles in the evaluation of PhD and Post-doctoral grants for FCT, PT, where I was Chair of the Experimental Biology and Biochemistry from 2016 to 2018, and I was Vice-Chair of the EX4 (Human biology and medical sciences) discipline panel for evaluation of EXPRO Grants from the Czech Science Foundation in 2020, 2021, and 2022.

Appendix I – List of scientific publications in peer-reviewed ISI journals

(The citations were taken from Scopus in 20211207)

 

128) Galocha, M, Viana, R, Pais, P, Silva-Dias, A, Cavalheiro, M, Miranda, IM, Van Ende, M, Souza, CS, Costa, C, Soares, CM, Van Dijck, P, Rodrigues, AG, Teixeira, MC (2021) “Genomic evolution towards azole resistance in Candida glabrata clinical isolates unveils the importance of CgHxt4/6/7 in azole accumulation”, Comms. Bio., accepted

 

127) Valério, M, Borges-Araújo, L, Melo, MN, Lousa, D, Soares*, CM (2022) “SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility”, Front. Med. Technol., 4:1009451., also in https://biorxiv.org/cgi/content/short/2021.11.30.470470v1

        https://10.3389/fmedt.2022.1009451

 

126) Valério, M, Mendonça, DA, Morais, J, Buga, CC, Cruz, CH, Castanho, MARB, Melo, MN, Soares*, CM, Veiga*, AS, Lousa*, D (2022) “Parainfluenza fusion peptide promotes membrane fusion by assembling into oligomeric pore-like structures”, ACS Chem. Biol., 17, 1831-1843. (joint corresponding author; Journal Cover)

        https://doi.org/10.1021/acschembio.2c00208

 

125) Marques, MC, Lousa, D, Silva, PM, Faustino, AF, Soares, CM, Santos, NC (2022) “The importance of lipid conjugation on anti-fusion peptides against Nipah virus”, Biomedicines, 10, 703

https://doi.org/10.3390/biomedicines10030703

 

124) Saramago, M, Costa, VG, Souza, CS, Bárria, C, Domingues, S, Viegas, S, Lousa, D, Soares, CM, Arraiano, CM, Matos, RG (2022) “The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs”, Microorganisms, 12, 342

https://doi.org/10.3390/microorganisms10020342

 

123) Lousa, D, Soares, CM (2021) “Molecular mechanisms of the influenza fusion peptide: insights from experimental and simulation studies”, FEBS Open Bio, 11, 3253-3261 (https://doi.org/10.1002/2211-5463.13323)

        Number of citations: 0

 

122) Martins, MC, Fernandes, SF, Salgueiro, BA, Soares, SC, Romão, CV, Soares, CM, Lousa, D, Folgosa, F, Teixeira, M (2021) “The amino acids motif –32GSSYN36- in the catalytic domain of E. coli flavorubredoxin NO reductase is essential for its activity”, Catalysts, 11(8), 926

        Number of citations: 0

https://doi.org/10.3390/catal11080926

 

121) Alenquer, M, Ferreira, F, Lousa, D, Valério, M, Medina-Lopes, M, Bergman, M-L, Gonçalves, J, Demengeot, J, Leite, RB, Lilue, J, Ning, Z, Penha-Gonçalvez, C, Soares, H, Soares, CMS, Amorim, MJ (2021) “Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies”, Plos Pathogens, 17(8): e1009772. (https://doi.org/10.1371/journal.ppat.1009772)

        Number of citations: 4

 

120) Saramago, M, Bárria, C, Costa, V, Souza, CS, Viegas, SC, Domingues, S, Lousa, D, Soares, CM, Arraiano, CM, Matos, RG (2021) “New targets for drug design: Importance of nsp14/nsp10 complex 1 formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2”, FEBS J., 288, 5130-5147

        Number of citations: 4

 

119) Abreu, B, Cruz, C, Oliveira, ASF, Soares, CM (2020) “ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer”, Sci.Rep., 11, 10591

        Number of citations: 0

 

118) Lousa, D, Pinto, ART, Campos, SRR, Baptista, AM, Veiga, AS, Castanho, MARB, Soares, CM (2020) “Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment”, Sci.Rep., 10, 20082

        Number of citations: 5

 

117) da Silva, JA, Meneghetti, M., Soares, CM (2020) “Molecular Dynamics Simulations suggest a Possible Role for NO in the Polyol Synthesis of Silver Nanostructures”, J.Phys.Chem.C, 124, 24279-24288

        Number of citations: 1

 

116) Barbosa, TM, Baltazar, CSA, Cruz, DR, Lousa, D, Soares, CM (2020) “Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases”, Sci.Rep., 10, 10540

        Number of citations: 0

 

115) Abreu, B, Lopes, EF, Oliveira, ASF, Soares, CM (2020) “The mutation F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis”, Proteins, 88, 113-126

        Number of citations: 3

 

114) Pereira, F, Nunes, F, Cruz, F, Fernandes, C, Isidro, A, Lousa, Soares, CM, Moran, C Henriques, A, Serrano, M (2019) “A LysM domain intervenes in sequential protein-protein and protein-peptidoglycan interactions important for spore coat assembly in Bacillus subtilis”, J.Bact., 201, e00642-18.

        Number of citations: 10

 

113) Duarte, AG, Catarino, T, Whitec, GF, Lousa, D, Neukirchen, S, Soares, CM, Sousa, FL, Clarke, TA, Pereira, IAC (2018) “An electrogenic redox loop in sulfate reduction reveals an ancient and widespread mechanism of energy conservation”, Nature Comm., 9:5448

        Number of citations: 13

 

112) Kaur, H, Abreu, B, Akhmetzyanov, D, Lakatos-Karoly, A; Soares, CM, Prisner, T, Glaubitz, C (2018) “Unexplored nucleotide binding modes for the ABC exporter MsbA”, JACS, 140, 14112–14125

        Number of citations: 12

 

111) Jeremias, HF, Lousa, D, Hollmann, A, Coelho, AC, Baltazar, CS, Seixas, JD, Marques, AR, Santos, NC, Romão, CC, Soares, CM (2018) “Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods”, PLOS One, 13(9): e0204624

        Number of citations: 7

 

110) Sena, F, Sousa, F, Oliveira, ASF, Soares, CM, Catarino, T, Pereira, MM (2018) “Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus”, Redox Biol., 16, 209-214

        Number of citations: 8

 

109) Velada, I, Grzebelus, D, Lousa, D, Soares, CM, Peixe, A, Arnholdt-Schmitt, B, Cardoso, HG (2018) “AOX1-subfamily gene members in Olea europaea cv. ‘Galega vulgar’ - Gene characterization and expression of transcripts during IBA-induced in vitro adventitious rooting.”, Int.J.Mol.Sci., 19, 597

        Number of citations: 12

 

108) Almadanim, MC, Gonçalves, NM, Rosa, MTG, Alexandre, BM, Cordeiro, AM, Rodrigues, M, Saibo, NJM, Soares, CM, Romão, CV, Oliveira, MM, Abreu, IA (2018) “The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications”, BBA Molecular Cell Research, 1865, 231-246.

        Number of citations: 22

 

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

        Number of citations: 9

 

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

        Number of citations: 7

 

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.

        Number of citations: 3

 

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

        Number of citations: 14

 

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., 428, 4686-4707

Number of citations: 18

 

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.

Number of citations: 7

 

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.

        Number of citations: 15

 

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

                Number of citations: 13

 

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

        Number of citations: 24

 

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

        Number of citations: 20

 

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

        Number of citations: 5

 

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

        Number of citations: 20

 

95) Paquete, CM, Fonseca, BM, Cruz, DR, Pereira, T, Pacheco, I, Soares, CM, Louro, RO (2014) “Exploring the molecular mechanisms of electron shuttling across the microbe/metal space”, Frontiers in Microbiology, 5, 318.

        Number of citations: 42

 

94) Damas, JM, Baptista, AM, Soares, CM (2014) “The Pathway for O-2 Diffusion inside CotA Laccase and Possible Implications on the Multicopper Oxidases Family”, J Chem Theor Comp, 10, 3525–3531

        Number of citations: 10

 

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)

        Number of citations: 3

 

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

        Number of citations: 21

 

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

        Number of citations: 36

 

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.

        Number of citations: 16

 

89) Gutiérrez-Sanz, O, Marques, MC, Baltazar, CSA, Fernández, VM, Soares, CM, Pereira, IAC, De Lacey, AL (2013) “Influence of the protein structure surrounding the active site on the catalytic activity of [NiFeSe] hydrogenases”, JBIC, 18, 419-427

        Number of citations: 19

 

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.

        Number of citations: 77

 

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

        Number of citations: 8

 

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

        Number of citations: 28

 

85) Campos, E, Asandei, A, McVey, CE, Dias, JC, Oliveira, ASF, Soares, CM, Luchian, T, and Astier, Y (2012) “The Role of Lys147 in the Interaction between MPSA-Gold Nanoparticles and the α-Hemolysin Nanopore”, Langmuir, 28, 15643-50

        Number of citations: 16

 

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

        Number of citations: 7

 

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

        Number of citations: 35

 

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

        Number of citations: 22

 

81) Azoia, NG, Fernandes, MM, Micaelo, NM, Soares, CM, Cavaco-Paulo, A (2012) “Molecular modeling of hair keratin/peptide complex: using MM-PBSA calculations to describe experimental binding results”, Proteins, 80, 1409-1417

                Number of citations: 11

 

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, 68, 186-193. (joint corresponding author).

        Number of citations: 24

 

79) Soares*, CM, Baptista, AM (2012) “Simulation of multihaem cytochromes”, FEBS Lett., 586, 510-518.

        Number of citations: 12

 

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

        Number of citations: 31

 

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

        Number of citations: 10

 

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

        Number of citations: 37

 

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

        Number of citations: 56

 

74) Baltazar, C, Marques, MC, Soares, CM, DeLacey, AM, Pereira, IAC, Matias, PM (2011) “Nickel-Iron-Selenium Hydrogenases - An Overview”, Eur.J.Inor.Chem., 2011, 948-962.

        Number of citations: 70

 

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.

        Number of citations: 11

 

72) Machuqueiro, M, Campos, SRR, Soares, CM, Baptista, AM (2010) “Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations”, J Phys Chem B, 114, 11659–11667

        Number of citations: 18

 

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.

        Number of citations: 62

 

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

        Number of citations: 36

 

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

        Number of citations: 32

 

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

        Number of citations: 10

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

        Number of citations: 16

 

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

        Number of citations: 39

 

65) Escrevente, C, Morais, VA, Keller, S, Soares, CM, Altevogt, P, Costa, J (2008) “Functional role of N-glycosylation from ADAM10 in processing, activity, stability and localization of the enzyme”, BBA, 1780, 905-913

        Number of citations: 59

 

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

        Number of citations: 54

 

63) Micaelo, NM, Soares, CM (2008) “Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies”. J.Phys.Chem.B, 112, 2566-2572

        Number of citations: 172

 

62) Micaelo, NM, Victor, BL, Soares, CM (2008) “Protein thermal stabilization by charged compatible solutes. Computational studies in rubredoxin from Desulfovibrio gigas”, Proteins, 72, 580-588

        Number of citations: 0

 

61) Rodrigues, JV, Victor, BL, Huber, H, Saraiva, LM, Soares, CM, Cabelli, DE, Teixeira, M (2008) “Superoxide reduction by Nanoarchaeum equitans neelaredoxin, a “natural mutant” lacking the ferric sixth ligand glutamate”, JBIC, 13, 219-228

        Number of citations: 21

 

60) Teixeira, VH, Soares, CM, Baptista, AM (2008) “Proton Pathways in a [NiFe]-Hydrogenase: A Theoretical Study", Proteins, 70, 1010-1022

        Number of citations: 52

 

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

        Number of citations: 33

 

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

        Number of citations: 4

 

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

        Number of citations: 15

 

56) Fernandes, AT, Soares, CM, Pereira, MM, Huber, R, Grass, G, Martins, LO (2007) “A robust metallo-oxidase from the hyperthermophilic bacterium Aquifex aeolicus”, FEBS J., 274, 2683-2694.

        Number of citations: 39

 

55) Micaelo, N, Soares, CM (2007) “Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents”, FEBS J., 274, 2424-2436.

        Number of citations: 81

 

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.

        Number of citations: 124

 

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 (J Iley and R Moreira are the corresponding authors)

        Number of citations: 7

 

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

        Number of citations: 78

 

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

        Number of citations: 13

 

50) Micaelo, NM, Baptista, AM, Soares, CM (2006) “Parameterization of 1-Butyl-3-Methylimidazolium Hexafluorophosphate/Nitrate Ionic Liquid for the GROMOS force field”, J.Phys.Chem.B, 110, 14444-14451.

        Number of citations: 123

 

49) Teixeira, VH, Baptista, AM, Soares, CM (2006) “Pathways of H2 towards the active site of [NiFE]-hydrogenase”, Biophys.J., 91, 2035-45.

        Number of citations: 61

 

48) Franco, IS, Mota, LJ, Soares, CM, Sá-Nogueira, I (2006) “Functional 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

        Number of citations: 22

 

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.

Number of citations: 15

 

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.

        Number of citations: 75

 

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.

        Number of citations: 20

 

44) Teixeira, VH, Cunha, CA, Machuqueiro, M, Oliveira, ASF, Victor, BL, Soares, CM, Baptista, AM (2005) “On the use of different dielectric constants for intrinsic and pairwise term in Poisson-Boltzmann studies of protein ionisation equilibrium.”, J.Phys.Chem.B, 109, 14691-14706.

        Number of citations: 70

 

43) Micaelo, NM, Teixeira, VH, Baptista, AM, Soares, CM (2005) “Water dependent properties of cutinase in nonaqueous solvents. A computational study of enantioselectivity.”, Biophys.J., 89, 999-1008.

        Number of citations: 38

 

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.

        Number of citations: 51

 

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.

        Number of citations: 23

 

40) Matias, PM, Pereira, IAC, Soares, CM, Carrondo, MA (2005) "Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview", Prog.Biophys.Mol.Biol., 89, 292-329.

        Number of citations: 106

 

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.

        Number of citations: 8

 

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

        Number of citations: 25

 

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

        Number of citations: 17

 

36) Soares*, CM, Baptista, AM, Pereira, MM, Teixeira, M. (2004) "Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase. Comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase", JBIC, 9, 124-134

        Number of citations: 23

 

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

        Number of citations: 28

 

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

        Number of citations: 20

 

33) Price, NJ, Pinheiro, C, Soares, CM, Ashford, D, Brownleader, M, Ricardo, CP, Jackson, P (2003) "A biochemical and molecular characterisation of LEP1, an extensin peroxidase from lupin", J.Biol.Chem., 278, 41389-41399

        Number of citations: 49

 

32) Bento, I, Teixeira, VH, Baptista, AM, Soares, CM, Matias, PM, Carrondo, MA (2003) "Redox-Bohr and other cooperativity effects in the nine heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies", J.Biol.Chem., 278, 36455-36469

Number of citations: 21

 

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

        Number of citations: 19

 

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

        Number of citations: 111

 

29) Baptista, AM, Teixeira, VH, Soares, CM (2002) "Constant-pH molecular dynamics using stochastic titration", J.Chem.Phys., 117, 4184-4200 (AM Baptista is the corresponding author)

        Number of citations: 227

 

28) Martins, LO, Soares, CM, Pereira, MM, Teixeira, M, Costa, T, Jones, GH, Henriques, AO (2002) "Molecular and biochemical characterization of a highly stable bacterial laccase which occurs as a structural component of the Bacillus subtilis endospore coat", J.Biol.Chem., 277, 18849-18859

        Number of citations: 428

 

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

        Number of citations: 52

 

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

        Number of ciations: 33

 

25) Abreu, IA, Saraiva, LM, Soares, CM, Teixeira, M, Cabelli, DE (2001) "The mechanism of superoxide scavenging by Archaeoglobus fulgidus neelaredoxin", J.Biol.Chem., 276, 38995-39001

        Number of citations: 48

 

24) Mendes, J, Baptista, AM, Carrondo, MA, Soares, CM (2001) "Implicit solvation in the Self-Consistent Mean Field Theory method: side-chain modelling and prediction of folding free energies of protein mutants", J.Comp.Aid.Mol.Des., 15, 721-740

        Number of citations: 16

 

23) Mendes, J, Nagarajaram, HA, Soares, CM, Blundell, TL, Carrondo, MA (2001) "Incorporing a knowledge-based bias into an energy-based side-chain modelling method: application to comparative modelling of protein structure", Biopolymers, 59, 72-86

        Number of citations: 19

 

22) Santana, M, Pereira, MM, Elias, NP, Soares, CM, Teixeira, M (2001) " Gene cluster of Rhodothermus marinus high-potential iron-sulfur protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases ", J.Bacteriology, 183, 687-699

        Number of citations: 33

 

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

        Number of citations: 100

 

20) Matias, PM, Soares, CM, Saraiva, LM, Coelho, R, Morais, J, LeGall, J, Carrondo, MA (2001) "[NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: primary sequence determination, crystallographic refinement at 1.8 Å and modelling studies of its interaction with the tetra-haem cytochrome c3", JBIC, 6, 63-81

        Number of citations: 179

 

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

        Number of citations: 9

 

18) Power, DM, Elias, NP, Richardson, SJ, Mendes, J, Soares, CM, Santos, CRA (2000) "Evolution of the Thyroid Hormone Binding Protein, Transthyretin", Gen. Comp. Endocrinol., 119, 241-255

        Number of citations: 149

 

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

        Number of citations: 80

 

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

        Number of citations: 41

 

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

        Number of citations: 40

 

14) Pereira, MM, Santana, M, Soares, CM, Mendes, J, Carita, JN, Saraste, M, Carrondo, MA, Teixeira, M (1999) “The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus”, BBA, 1413, 1-13.

        Number of citations: 46

 

13) Mendes, J, Baptista, AM and Carrondo, MA, Soares, CM (1999) "Improved modelling of side-chains in proteins with rotamer-based methods: a flexible rotamer model.", Proteins, 37, 530-543.

        Number of citations: 68

 

12) Cunha, CA, Romão, MJ, Sadeghi, SJ, Valetti, F, Gilardi, G, Soares, CM (1999) “Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes”, JBIC, 4, 360-374

        Number of citations: 21

 

11) Baptista, AM, Martel, PJ, Soares, CM (1999) “Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics”, Biophys.J., 76, 2978-2998. (AM Baptista is the corresponding author)

        Number of citations: 91

 

10) Martel, PJ, Soares, CM, Baptista, AM, Fuxreiter, M, Náray-Szabó, G, Louro, RO, Carrondo, MA (1999) “Comparative redox and pKa calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods.”, JBIC, 4, 73-86

        Number of citations: 36

 

9) Petukhov, M, Cregut, D, Soares, CM, Serrano, L (1999) “Local water bridges and protein conformational stability”, Prot.Sci., 8, 1982-1989

        Number of citations: 59

 

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

        Number of citations: 42

 

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

        Number of citations: 34

6) Soares*, CM, Martel, PJ, Mendes, J, Carrondo, MA (1998) “Molecular dynamics simulation of cytochrome c3. Studying the reduction processes using free energy calculations”, Biophys.J., 74, 1708-1721

Number of citations: 30

 

5) Soares*, CM, Martel, PJ, Carrondo, MA (1997) “Theoretical studies on the redox-Bohr effect in cytochrome c3 from  Desulfovibrio vulgaris Hildenborough”. JBIC, 2, 714-727

        Number of citations: 30

 

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 and comparison with plastocyanin.”, Structure, 3, 1159-1169

        Number of citations: 127

 

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

        Number of citations: 40

 

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

        Number of citations: 3

 

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

        Number of citations: 31