Artigo em revista |
- Lucie da Rocha; António M. Baptista; Sara R. R. Campos. "Computational Study of the pH-Dependent Ionic Environment around
ß-Lactoglobulin". The Journal of Physical Chemistry B (2022): https://doi.org/10.1021/acs.jpcb.2c03797.
10.1021/acs.jpcb.2c03797
- António M. Baptista; Lucie da Rocha; Sara R. R. Campos. "FixBox: A General Algorithm to Fix Molecular Systems in Periodic
Boxes". Journal of Chemical Information and Modeling (2022): https://doi.org/10.1021/acs.jcim.2c00823.
10.1021/acs.jcim.2c00823
- Lucie da Rocha; António M. Baptista; Sara R. R. Campos. "Correction to “Approach to Study pH-Dependent Protein Association
Using Constant-pH Molecular Dynamics: Application to the Dimerization of ß-Lactoglobulin”". Journal of Chemical Theory
and Computation (2022): https://doi.org/10.1021/acs.jctc.2c00605.
10.1021/acs.jctc.2c00605
- Lucie da Rocha; António M. Baptista; Sara R. R. Campos. "Approach to Study pH-Dependent Protein Association Using Constant-pH
Molecular Dynamics: Application to the Dimerization of ß-Lactoglobulin". Journal of Chemical Theory and Computation
(2022): https://doi.org/10.1021/acs.jctc.1c01187.
10.1021/acs.jctc.1c01187
- Lousa, D.; Pinto, A.R.T.; Campos, S.R.R.; Baptista, A.M.; Veiga, A.S.; Castanho, M.A.R.B.; Soares, C.M.. "Effect of pH on
the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment".
Scientific Reports 10 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85096181420&partnerID=MN8TOARS.
10.1038/s41598-020-77040-y
- Diogo Vila-Viçosa; Pedro B. P. S. Reis; António M. Baptista; Chris Oostenbrink; Miguel Machuqueiro. "A pH Replica Exchange
Scheme in the Stochastic Titration Constant-pH MD Method". Journal of Chemical Theory and Computation (2019): https://doi.org/10.1021/acs.jctc.9b00030.
10.1021/acs.jctc.9b00030
- Nicoletta Liguori; Sara R. R. Campos; António M. Baptista; Roberta Croce. "Molecular Anatomy of Plant Photoprotective Switches:
The Sensitivity of PsbS to the Environment, Residue by Residue". The Journal of Physical Chemistry Letters (2019):
1737-1742. https://doi.org/10.1021/acs.jpclett.9b00437.
10.1021/acs.jpclett.9b00437
- Pedro B. P. S. Reis; Diogo Vila-Viçosa; Sara R. R. Campos; António M. Baptista; Miguel Machuqueiro. "Role of Counterions in
Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers". ACS Omega (2018): https://doi.org/10.1021/acsomega.7b01708.
10.1021/acsomega.7b01708
- Magalhães, P.R.; Oliveira, A.S.F.; Campos, S.R.R.; Soares, C.M.; Baptista, A.M.. "Effect of a pH Gradient on the Protonation
States of Cytochrome c Oxidase: A Continuum Electrostatics Study". Journal of Chemical Information and Modeling 57
2 (2017): 256-266. http://www.scopus.com/inward/record.url?eid=2-s2.0-85014290827&partnerID=MN8TOARS.
10.1021/acs.jcim.6b00575
- Campos, S.R.R.; Iranzo, O.; Baptista, A.M.. "Constant-pH MD Simulations Portray the Protonation and Structural Behavior of
Four Decapeptides Designed to Coordinate Cu2+". Journal of Physical Chemistry B 120 6 (2016): 1080-1091.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84959440690&partnerID=MN8TOARS.
10.1021/acs.jpcb.5b12052
- Conceição, K.; Magalhães, P.R.; Campos, S.R.R.; Domingues, M.M.; Ramu, V.G.; Michalek, M.; Bertani, P.; et al. "The anti-inflammatory
action of the analgesic kyotorphin neuropeptide derivatives: Insights of a lipid-mediated mechanism". Amino Acids 48
1 (2016): 307-318. http://www.scopus.com/inward/record.url?eid=2-s2.0-84955207969&partnerID=MN8TOARS.
10.1007/s00726-015-2088-9
- Filipe, L.C.S.; Campos, S.R.R.; Machuqueiro, M.; Darbre, T.; Baptista, A.M.. "Structuring peptide dendrimers through pH modulation
and substrate binding". Journal of Physical Chemistry B 120 38 (2016): 10138-10152. http://www.scopus.com/inward/record.url?eid=2-s2.0-84992322845&partnerID=MN8TOARS.
10.1021/acs.jpcb.6b05905
- Oliveira, A.S.F.; Campos, S.R.R.; Baptista, A.M.; Soares, C.M.. "Coupling between protonation and conformation in cytochrome
c oxidase: Insights from constant-pH MD simulations". Biochimica et Biophysica Acta - Bioenergetics 1857 6 (2016):
759-771. http://www.scopus.com/inward/record.url?eid=2-s2.0-84964689558&partnerID=MN8TOARS.
10.1016/j.bbabio.2016.03.024
- de Barros, D.P.C.; Campos, S.R.R.; Azevedo, A.M.; Baptista, A.M.; Aires-Barros, M.R.. "Predicting protein partition coefficients
in aqueous two phase system". Journal of Chromatography A 1470 (2016): 50-58. http://www.scopus.com/inward/record.url?eid=2-s2.0-84995380022&partnerID=MN8TOARS.
10.1016/j.chroma.2016.09.072
- Filipe, L.C.S.; Machuqueiro, M.; Darbre, T.; Baptista, A.M.. "Exploring the Structural Properties of Positively Charged Peptide
Dendrimers". Journal of Physical Chemistry B 120 43 (2016): 11323-11330. http://www.scopus.com/inward/record.url?eid=2-s2.0-85032160899&partnerID=MN8TOARS.
10.1021/acs.jpcb.6b09156
- Correia, M.; Snabe, T.; Thiagarajan, V.; Petersen, S.B.; Campos, S.R.R.; Baptista, A.M.; Neves-Petersen, M.T.. "Erratum: Photonic
activation of plasminogen induced by low dose UVB (PLoS ONE (2015) 10:12 (e0144794))". PLoS ONE 10 12 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84957109767&partnerID=MN8TOARS.
10.1371/journal.pone.0144794
- Santos, H.A.F.; Vila-Viçosa, D.; Teixeira, V.H.; Baptista, A.M.; Machuqueiro, M.. "Constant-pH MD Simulations of DMPA/DMPC
Lipid Bilayers". Journal of Chemical Theory and Computation 11 12 (2015): 5973-5979. http://www.scopus.com/inward/record.url?eid=2-s2.0-84949633293&partnerID=MN8TOARS.
10.1021/acs.jctc.5b00956
- Carvalheda, C.A.; Campos, S.R.R.; Baptista, A.M.. "The Effect of Membrane Environment on Surfactant Protein C Stability Studied
by Constant-pH Molecular Dynamics". Journal of Chemical Information and Modeling 55 10 (2015): 2206-2217. http://www.scopus.com/inward/record.url?eid=2-s2.0-84945581645&partnerID=MN8TOARS.
10.1021/acs.jcim.5b00076
- Correia, M.; Snabe, T.; Thiagarajan, V.; Petersen, S.B.; Campos, S.R.R.; Baptista, A.M.; Neves-Petersen, M.T.. "Photonic activation
of plasminogen induced by low dose UVB". PLoS ONE 10 1 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84922108038&partnerID=MN8TOARS.
10.1371/journal.pone.0116737
- Carvalheda, C.A.; Campos, S.R.R.; Machuqueiro, M.; Baptista, A.M.. "Correction to "structural effects of pH and deacylation
on surfactant protein C in an organic solvent mixture: A constant-pH MD study"". Journal of Chemical Information and Modeling
55 1 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84921826482&partnerID=MN8TOARS.
10.1021/ci5007454
- Vila-Viçosa, D.; Teixeira, V.H.; Baptista, A.M.; Machuqueiro, M.. "Constant-pH MD simulations of an oleic acid bilayer". Journal
of Chemical Theory and Computation 11 5 (2015): 2367-2376. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929155290&partnerID=MN8TOARS.
10.1021/acs.jctc.5b00095
- Magalhães, P.R.; Machuqueiro, M.; Baptista, A.M.. "Constant-pH molecular dynamics study of kyotorphin in an explicit bilayer".
Biophysical Journal 108 9 (2015): 2282-2290. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929660265&partnerID=MN8TOARS.
10.1016/j.bpj.2015.03.052
- Vila-Vic¸osa, D.; Teixeira, V.H.; Santos, H.A.F.; Baptista, A.M.; Machuqueiro, M.. "Treatment of ionic strength in biomolecular
simulations of charged lipid bilayers". Journal of Chemical Theory and Computation 10 12 (2014): 5483-5492. http://www.scopus.com/inward/record.url?eid=2-s2.0-84916241903&partnerID=MN8TOARS.
10.1021/ct500680q
- De Barros, D.P.C.; Campos, S.R.R.; Madeira, P.P.; Azevedo, A.M.; Baptista, A.M.; Aires-Barros, M.R.. "Modeling the partitioning
of amino acids in aqueous two phase systems". Journal of Chromatography A 1329 (2014): 52-60. http://www.scopus.com/inward/record.url?eid=2-s2.0-84895141345&partnerID=MN8TOARS.
10.1016/j.chroma.2013.12.015
- Oliveira, A.S.F.; Damas, J.M.; Baptista, A.M.; Soares, C.M.. "Exploring O2Diffusion in A-Type Cytochrome c Oxidases:
Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site". PLoS Computational Biology
10 12 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84919667074&partnerID=MN8TOARS.
10.1371/journal.pcbi.1004010
- Damas, J.M.; Baptista, A.M.; Soares, C.M.. "The pathway for O2 diffusion inside CotA laccase and possible implications on
the multicopper oxidases family". Journal of Chemical Theory and Computation 10 8 (2014): 3525-3531. http://www.scopus.com/inward/record.url?eid=2-s2.0-84906245108&partnerID=MN8TOARS.
10.1021/ct500196e
- Teixeira, V.H.; Vila-Viccosa, D.; Baptista, A.M.; Machuqueiro, M.. "Protonation of DMPC in a bilayer environment using a linear
response approximation". Journal of Chemical Theory and Computation 10 5 (2014): 2176-2184. http://www.scopus.com/inward/record.url?eid=2-s2.0-84900529268&partnerID=MN8TOARS.
10.1021/ct5000082
- Damas, J.M.; Filipe, L.C.S.; Campos, S.R.R.; Lousa, D.; Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Predicting the thermodynamics
and kinetics of helix formation in a cyclic peptide model". Journal of Chemical Theory and Computation 9 11 (2013):
5148-5157. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887835236&partnerID=MN8TOARS.
10.1021/ct400529k
- Filipe, L.C.S.; Machuqueiro, M.; Darbre, T.; Baptista, A.M.. "Unraveling the conformational determinants of peptide dendrimers
using molecular dynamics simulations". Macromolecules 46 23 (2013): 9427-9436. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890366302&partnerID=MN8TOARS.
10.1021/ma401574b
- Carvalheda, C.A.; Campos, S.R.R.; Machuqueiro, M.; Baptista, A.M.. "Structural effects of ph and deacylation on surfactant
protein c in an organic solvent mixture: A constant-pH MD study". Journal of Chemical Information and Modeling 53 11
(2013): 2979-2989. http://www.scopus.com/inward/record.url?eid=2-s2.0-84888621173&partnerID=MN8TOARS.
10.1021/ci400479c
- Lousa, D.; Baptista, A.M.; Soares, C.M.. "A molecular perspective on nonaqueous biocatalysis: Contributions from simulation
studies". Physical Chemistry Chemical Physics 15 33 (2013): 13723-13736. http://www.scopus.com/inward/record.url?eid=2-s2.0-84881248110&partnerID=MN8TOARS.
10.1039/c3cp51761f
- Filipe, L.C.S.; MacHuqueiro, M.; Baptista, A.M.. "Erratum: Unfolding the conformational behavior of peptide dendrimers: Insights
from molecular dynamics simulations (Journal of the American Chemical Society (2011) 133 (5042-5052) DOI: 10.1021/ja111001v)".
Journal of the American Chemical Society 134 49 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84870946509&partnerID=MN8TOARS.
10.1021/ja311198h
- Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Structural determinants for the membrane insertion of the transmembrane peptide
of hemagglutinin from influenza virus". Journal of Chemical Information and Modeling 52 11 (2012): 3001-3012. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870015416&partnerID=MN8TOARS.
10.1021/ci3003396
- Soares, C.M.; Baptista, A.M.. "Simulation of multihaem cytochromes". FEBS Letters 586 5 (2012): 510-518. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857916893&partnerID=MN8TOARS.
10.1016/j.febslet.2011.10.019
- Mateus, P.; Delgado, R.; Groves, P.; Campos, S.R.R.; Baptista, A.M.; Brandão, P.; Félix, V.. "Water encapsulation in a polyoxapolyaza
macrobicyclic compound". Journal of Organic Chemistry 77 16 (2012): 6816-6824. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865230787&partnerID=MN8TOARS.
10.1021/jo300799s
- Lousa, D.; Baptista, A.M.; Soares, C.M.. "Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using
molecular dynamics simulations". Journal of Chemical Information and Modeling 52 2 (2012): 465-473. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857583770&partnerID=MN8TOARS.
10.1021/ci200455z
- Vila-Viçosa, D.; Campos, S.R.R.; Baptista, A.M.; MacHuqueiro, M.. "Reversibility of prion misfolding: Insights from constant-PH
molecular dynamics simulations". Journal of Physical Chemistry B 116 30 (2012): 8812-8821. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864755277&partnerID=MN8TOARS.
10.1021/jp3034837
- Lousa, D.; Cianci, M.; Helliwell, J.R.; Halling, P.J.; Baptista, A.M.; Soares, C.M.. "Interaction of counterions with subtilisin
in acetonitrile: Insights from molecular dynamics simulations". Journal of Physical Chemistry B 116 20 (2012): 5838-5848.
http://www.scopus.com/inward/record.url?eid=2-s2.0-84862279541&partnerID=MN8TOARS.
10.1021/jp303008g
- Filipe, L.C.S.; MacHuqueiro, M.; Baptista, A.M.. "Unfolding the conformational behavior of peptide dendrimers: Insights from
molecular dynamics simulations". Journal of the American Chemical Society 133 13 (2011): 5042-5052. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953908369&partnerID=MN8TOARS.
10.1021/ja111001v
- Alexov, E.; Mehler, E.L.; Baker, N.; M. Baptista, A.; Huang, Y.; Milletti, F.; Erik Nielsen, J.; et al. "Progress in the prediction
of pK a values in proteins". Proteins: Structure, Function and Bioinformatics 79 12 (2011): 3260-3275. http://www.scopus.com/inward/record.url?eid=2-s2.0-81055157643&partnerID=MN8TOARS.
10.1002/prot.23189
- Machuqueiro, M.; Baptista, A.M.. "Is the prediction of pK a values by constant-pH molecular dynamics being hindered by inherited
problems?". Proteins: Structure, Function and Bioinformatics 79 12 (2011): 3437-3447. http://www.scopus.com/inward/record.url?eid=2-s2.0-81055140448&partnerID=MN8TOARS.
10.1002/prot.23115
- Lousa, D.; Baptista, A.M.; Soares, C.M.. "Structural determinants of ligand imprinting: A molecular dynamics simulation study
of subtilisin in aqueous and apolar solvents". Protein Science 20 2 (2011): 379-386. http://www.scopus.com/inward/record.url?eid=2-s2.0-79251557782&partnerID=MN8TOARS.
10.1002/pro.569
- Damas, J.M.; Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Structural consequences of ATP hydrolysis on the ABC transporter
NBD dimer: Molecular dynamics studies of HlyB". Protein Science 20 7 (2011): 1220-1230. http://www.scopus.com/inward/record.url?eid=2-s2.0-79959352522&partnerID=MN8TOARS.
10.1002/pro.650
- Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Inter-domain communication mechanisms in an ABC importer: A molecular dynamics
study of the MalFGK 2E complex". PLoS Computational Biology 7 8 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80052311546&partnerID=MN8TOARS.
10.1371/journal.pcbi.1002128
- Oliveira, A.S.; Baptista, A.M.; Soares, C.M.. "Conformational changes induced by ATP-hydrolysis in an ABC transporter: A molecular
dynamics study of the Sav1866 exporter". Proteins: Structure, Function and Bioinformatics 79 6 (2011): 1977-1990. http://www.scopus.com/inward/record.url?eid=2-s2.0-79955741987&partnerID=MN8TOARS.
10.1002/prot.23023
- Campos, S.R.R.; Baptista, A.M.. "Erratum: Conformational analysis in a multidimensional energy landscape: Study of an arginylglutamate
repeat (Journal of Physical Chemistry B (2009) 113 (15989))". Journal of Physical Chemistry B 114 23 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77953449669&partnerID=MN8TOARS.
10.1021/jp103633j
- Campos, S.R.R.; MacHuqueiro, M.; Baptista, A.M.. "Constant-pH molecular dynamics simulations reveal a ß-rich form of the human
prion protein". Journal of Physical Chemistry B 114 39 (2010): 12692-12700. http://www.scopus.com/inward/record.url?eid=2-s2.0-77957317648&partnerID=MN8TOARS.
10.1021/jp104753t
- MacHuqueiro, M.; Campos, S.R.R.; Soares, C.M.; Baptista, A.M.. "Membrane-induced conformational changes of kyotorphin revealed
by molecular dynamics simulations". Journal of Physical Chemistry B 114 35 (2010): 11659-11667. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956326420&partnerID=MN8TOARS.
10.1021/jp104418g
- Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Insights into the molecular mechanism of an ABC transporter: Conformational
changes in the NBD dimer of mj0796". Journal of Physical Chemistry B 114 16 (2010): 5486-5496. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951539821&partnerID=MN8TOARS.
10.1021/jp905735y
- Machuqueiro, M.; Baptista, A.M.. "Molecular dynamics at constant pH and reduction potential: Application to cytochrome c3".
Journal of the American Chemical Society 131 35 (2009): 12586-12594. http://www.scopus.com/inward/record.url?eid=2-s2.0-69849094447&partnerID=MN8TOARS.
10.1021/ja808463e
- Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:
Oxygen oxidoreductase from Desulfovibrio gigas". Journal of Biological Inorganic Chemistry 14 6 (2009): 853-862. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349289240&partnerID=MN8TOARS.
10.1007/s00775-009-0497-5
- Campos, S.R.R.; Baptista, A.M.. "Conformational analysis in a multidimensional energy landscape: Study of an arginylglutamate
repeat". Journal of Physical Chemistry B 113 49 (2009): 15989-16001. http://www.scopus.com/inward/record.url?eid=2-s2.0-71549167017&partnerID=MN8TOARS.
10.1021/jp902991u
- Veríssimo, A.F.; Sousa, F.L.; Baptista, A.M.; Teixeira, M.; Pereira, M.M.. "Thermodynamic redox behavior of the heme centers
in A-type heme-copper oxygen reductases: Comparison between the two subfamilies". Biophysical Journal 95 9 (2008):
4448-4455. http://www.scopus.com/inward/record.url?eid=2-s2.0-58149144256&partnerID=MN8TOARS.
10.1529/biophysj.108.139493
- Sousa, F.L.; Veríssimo, A.F.; Baptista, A.M.; Soulimane, T.; Teixeira, M.; Pereira, M.M.. "Redox properties of Thermus thermophilus
ba3: Different electron-proton coupling in oxygen reductases? (Biophysical Journal (2008) 94, (2434-2441)". Biophysical
Journal 95 1 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-61349111548&partnerID=MN8TOARS.
10.1529/biophysj.108.0900181
- Veríssimo, A.F.; Sousa, F.L.; Baptista, A.M.; Teixeira, M.; Pereira, M.M.. "Thermodynamic redox behavior of the heme centers
of cbb3 heme-copper oxygen reductase from Bradyrhizobium japonicum (Biochemistry (2007) 46, 46, (13245-13253))". Biochemistry
47 19 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-43249129717&partnerID=MN8TOARS.
10.1021/bi8005829
- Eberini, I.; Rocco, A.G.; Ientile, A.R.; Baptista, A.M.; Gianazza, E.; Tomaselli, S.; Molinari, H.; Ragona, L.. "Conformational
and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein". Proteins: Structure, Function
and Genetics 71 4 (2008): 1889-1898. http://www.scopus.com/inward/record.url?eid=2-s2.0-44349108965&partnerID=MN8TOARS.
10.1002/prot.21875
- Rocco, A.G.; Mollica, L.; Ricchiuto, P.; Baptista, A.M.; Gianazza, E.; Eberini, I.. "Characterization of the protein unfolding
processes induced by urea and temperature". Biophysical Journal 94 6 (2008): 2241-2251. http://www.scopus.com/inward/record.url?eid=2-s2.0-44049099949&partnerID=MN8TOARS.
10.1529/biophysj.107.115535
- Sousa, F.L.; Veríssimo, A.F.; Baptista, A.M.; Soulimane, T.; Teixeira, M.; Pereira, M.M.. "Redox properties of thermus thermophilus
ba3: Different electron-proton coupling in oxygen reductases?". Biophysical Journal 94 6 (2008): 2434-2441. http://www.scopus.com/inward/record.url?eid=2-s2.0-44049088504&partnerID=MN8TOARS.
10.1529/biophysj.107.122614
- Teixeira, V.H.; Soares, C.M.; Baptista, A.M.. "Proton pathways in a [NiFe]-hydrogenase: A theoretical study". Proteins:
Structure, Function and Genetics 70 3 (2008): 1010-1022. http://www.scopus.com/inward/record.url?eid=2-s2.0-38549139111&partnerID=MN8TOARS.
10.1002/prot.21588
- Machuqueiro, M.; Baptista, A.M.. "Acidic range titration of HEWL using a constant-pH molecular dynamics method". Proteins:
Structure, Function and Genetics 72 1 (2008): 289-298. http://www.scopus.com/inward/record.url?eid=2-s2.0-44949173075&partnerID=MN8TOARS.
10.1002/prot.21923
- Machuqueiro, M.; Baptista, A.M.. "The pH-dependent conformational states of kyotorphin: A constant-pH molecular dynamics study".
Biophysical Journal 92 6 (2007): 1836-1845. http://www.scopus.com/inward/record.url?eid=2-s2.0-33947640091&partnerID=MN8TOARS.
10.1529/biophysj.106.092445
- Gaspar, P.; Neves, A.R.; Shearman, C.A.; Gasson, M.J.; Baptista, A.M.; Turner, D.L.; Soares, C.M.; Santos, H.. "The lactate
dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties
- Comparative modeling to probe the molecular basis". FEBS Journal 274 22 (2007): 5924-5936. http://www.scopus.com/inward/record.url?eid=2-s2.0-35748951589&partnerID=MN8TOARS.
10.1111/j.1742-4658.2007.06115.x
- Veríssimo, A.F.; Sousa, F.L.; Baptista, A.M.; Teixeira, M.; Pereira, M.M.. "Thermodynamic redox behavior of the heme centers
of cbb3 heme-copper oxygen reductase from Bradyrhizobium japonicum". Biochemistry 46 46 (2007): 13245-13253. http://www.scopus.com/inward/record.url?eid=2-s2.0-36348983845&partnerID=MN8TOARS.
10.1021/bi700733g
- Rocha, R.; Leal, S.S.; Teixeira, V.H.; Regalla, M.; Huber, H.; Baptista, A.M.; Soares, C.M.; Gomes, C.M.. "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 34 (2006): 10376-10384. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748694511&partnerID=MN8TOARS.
10.1021/bi0610698
- Machuqueiro, M.; Baptista, A.M.. "Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling
in decalysine". Journal of Physical Chemistry B 110 6 (2006): 2927-2933. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644745556&partnerID=MN8TOARS.
10.1021/jp056456q
- Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Pathways of H2 toward the active site of [NiFe]-hydrogenase". Biophysical
Journal 91 6 (2006): 2035-2045. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748456960&partnerID=MN8TOARS.
10.1529/biophysj.106.084376
- Micaelo, N.M.; Baptists, A.M.; Soares, C.M.. "Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic
liquid for the GROMOS force field". Journal of Physical Chemistry B 110 29 (2006): 14444-14451. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746915678&partnerID=MN8TOARS.
10.1021/jp061869s
- Lopes, S.C.D.N.; Soares, C.M.; Baptista, A.M.; Goormaghtigh, E.; Cabral, B.J.C.; Castanho, M.A.R.B.. "Conformational and orientational
guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: Putative correlation toward receptor docking".
Journal of Physical Chemistry B 110 7 (2006): 3385-3394. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644895138&partnerID=MN8TOARS.
10.1021/jp053651w
- Oliveira, A.S.F.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Reorganization and conformational changes in the reduction
of tetraheme cytochromes". Biophysical Journal 89 6 (2005): 3919-3930. http://www.scopus.com/inward/record.url?eid=2-s2.0-28444483273&partnerID=MN8TOARS.
10.1529/biophysj.105.065144
- Teixeira, V.H.; Cunha, C.A.; Machuqueiro, M.; Oliveira, A.S.F.; Victor, B.L.; Soares, C.M.; Baptista, A.M.. "On the use of
different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization
equilibrium". Journal of Physical Chemistry B 109 30 (2005): 14691-14706. http://www.scopus.com/inward/record.url?eid=2-s2.0-23844500381&partnerID=MN8TOARS.
10.1021/jp052259f
- Micaelo, N.M.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Water dependent properties of cutinase in nonaqueous solvents:
A computational study of enantioselectivity". Biophysical Journal 89 2 (2005): 999-1008. http://www.scopus.com/inward/record.url?eid=2-s2.0-23244449490&partnerID=MN8TOARS.
10.1529/biophysj.105.063297
- Rivas, L.; Soares, C.M.; Baptista, A.M.; Simaan, J.; Di Paolo, R.E.; Murgida, D.H.; Hildebrandt, P.. "Electric-field-induced
redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: Surface-enhanced resonance raman
spectroscopy and simulation studies". Biophysical Journal 88 6 (2005): 4188-4199. http://www.scopus.com/inward/record.url?eid=2-s2.0-22244481835&partnerID=MN8TOARS.
10.1529/biophysj.104.057232
- Eberini, I.; Baptista, A.M.; Gianazza, E.; Fraternali, F.; Beringhelli, T.. "Reorganization in Apo- and Holo-ß-Lactoglobulin
Upon Protonation of Glu89: Molecular Dynamics and pKa Calculations". Proteins: Structure, Function and Genetics 54
4 (2004): 744-758. http://www.scopus.com/inward/record.url?eid=2-s2.0-1542316338&partnerID=MN8TOARS.
10.1002/prot.10643
- Bento, I.; Matias, P.M.; Baptista, A.M.; Da Costa, P.N.; Van Dongen, W.M.A.M.; Saraiva, L.M.; Schneider, T.R.; Soares, C.M.;
Carrondo, M.A.. "Molecular Basis for Redox-Bohr and Cooperative Effects in Cytochrome c 3 from Desulfovibrio desulfuricans
ATCC 27774: Crystallographic and Modeling Studies of Oxidized and Reduced High-Resolution Structures at pH 7.6". Proteins:
Structure, Function and Genetics 54 1 (2004): 135-152. http://www.scopus.com/inward/record.url?eid=2-s2.0-0348047621&partnerID=MN8TOARS.
10.1002/prot.10431
- Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Theoretical identification of proton channels in the quinol oxidase aa 3 from
Acidianus ambivalens". Biophysical Journal 87 6 (2004): 4316-4325. http://www.scopus.com/inward/record.url?eid=2-s2.0-10044240740&partnerID=MN8TOARS.
10.1529/biophysj.104.049353
- Soares, C.M.; Baptista, A.M.; Pereira, M.M.; Teixeira, M.. "Investigation of protonatable residues in Rhodothermus marinus
caa 3 haem-copper oxygen reductase: Comparism with Paracoccus denitrificans aa3 haem-copper oxygen reductase". Journal
of Biological Inorganic Chemistry 9 2 (2004): 124-134. http://www.scopus.com/inward/record.url?eid=2-s2.0-1542298196&partnerID=MN8TOARS.
10.1007/s00775-003-0509-9
- Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Modeling Electron Transfer Thermodynamics in Protein Complexes: Interaction
between Two Cytochromes c3". Biophysical Journal 86 5 (2004): 2773-2785. http://www.scopus.com/inward/record.url?eid=2-s2.0-2142644598&partnerID=MN8TOARS.
10.1016/S0006-3495(04)74331-3
- Bento, I.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.; Matias, P.M.; Carrondo, M.A.. "Redox-Bohr and other cooperativity
effects in the nine-heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and modeling studies".
Journal of Biological Chemistry 278 38 (2003): 36455-36469. http://www.scopus.com/inward/record.url?eid=2-s2.0-0141815636&partnerID=MN8TOARS.
10.1074/jbc.M301745200
- Soares, C.M.; Teixeira, V.H.; Baptista, A.M.. "Protein structure and dynamics in nonaqueous solvents: Insights from molecular
dynamics simulation studies". Biophysical Journal 84 3 (2003): 1628-1641. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037342275&partnerID=MN8TOARS.
- Teixeira, V.H.; Soares, C.M.; Baptista, A.M.. "Studies of the reduction and protonation behavior of tetraheme cytochromes
using atomic detail". Journal of Biological Inorganic Chemistry 7 1-2 (2002): 200-216. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036359052&partnerID=MN8TOARS.
10.1007/s007750100287
- Baptista, A.M.; Teixeira, V.H.; Soares, C.M.. "Constant-pH molecular dynamics using stochastic titration". Journal of Chemical
Physics 117 9 (2002): 4184-4200. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036732086&partnerID=MN8TOARS.
10.1063/1.1497164
- Baptista, A.M.. "Comment on "explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to
small amines" [J. Chem. Phys. 114, 9706 (2001)]". Journal of Chemical Physics 116 17 (2002): 7766-7768. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036573188&partnerID=MN8TOARS.
10.1063/1.1465399
- Louro, R.O.; Bento, I.; Matias, P.M.; Catarino, T.; Baptista, A.M.; Soares, C.M.; Carrondo, M.A.; Turner, D.L.; Xavier, A.V..
"Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome".
Journal of Biological Chemistry 276 47 (2001): 44044-44051. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035941269&partnerID=MN8TOARS.
10.1074/jbc.M107136200
- Mendes, J.; Baptista, A.M.; Carrondo, M.A.; Soares, C.M.. "Implicit solvation in the self-consistent mean field theory method:
Sidechain modelling and prediction of folding free energies of protein mutants". Journal of Computer-Aided Molecular Design
15 8 (2001): 721-740. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034748018&partnerID=MN8TOARS.
10.1023/A:1012279810260
- Baptista, A.M.; Scares, C.M.. "Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation
equilibrium of proteins". Journal of Physical Chemistry B 105 1 (2001): 293-309. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035120969&partnerID=MN8TOARS.
- Mendes, J.; Baptista, A.M.; Carrondo, M.A.; Soares, C.M.. "Improved modeling of side-chains in proteins with rotamer-based
methods: A flexible rotamer model". Proteins: Structure, Function and Genetics 37 4 (1999): 530-543. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032732306&partnerID=MN8TOARS.
10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H
- Martel, P.J.; Soares, C.M.; Baptista, A.M.; Fuxreiter, M.; Náray-Szabó, G.; Louro, R.O.; Carrondo, M.A.. "Comparative redox
and pK(a) calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods". Journal
of Biological Inorganic Chemistry 4 1 (1999): 73-86. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032588946&partnerID=MN8TOARS.
10.1007/s007750050291
- Baptista, A.M.; Martel, P.J.; Soares, C.M.. "Simulation of electron-proton coupling with a Monte Carlo method: Application
to cytochrome c3 using continuum electrostatics". Biophysical Journal 76 6 (1999): 2978-2998. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033001692&partnerID=MN8TOARS.
10.1016/S0006-3495(99)77452-7
- Baptista, A.M.; Jonson, P.H.; Hough, E.; Petersen, S.B.. "The origin of trypsin: Evidence for multiple gene duplications in
trypsins". Journal of Molecular Evolution 47 3 (1998): 353-362. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031718943&partnerID=MN8TOARS.
10.1007/PL00006393
- Baptista, A.M.; Martel, P.J.; Petersen, S.B.. "Simulation of protein conformational freedom as a function of pH: Constant-pH
molecular dynamics using implicit titration". Proteins: Structure, Function and Genetics 27 4 (1997): 523-544. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030970305&partnerID=MN8TOARS.
10.1002/(SICI)1097-0134(199704)27:4<523::AID-PROT6>3.0.CO;2-B
- Sebastião, M.J.; Martel, P.; Baptista, A.; Petersen, S.B.; Cabral, J.M.S.; Aires-Barros, M.R.. "Predicting the partition coefficients
of a recombinant cutinase in polyethylene glycol/phosphate aqueous two-phase systems". Biotechnology and Bioengineering
56 3 (1997): 248-257. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031555165&partnerID=MN8TOARS.
10.1002/(SICI)1097-0290(19971105)56:3<248::AID-BIT2>3.0.CO;2-J
- Jones, R.A.; Haraldseth, O.; Baptista, A.M.; Müller, T.B.; Øksendal, A.N.. "A study of the contribution of changes in the
cerebral blood volume to the haemodynamic response to anoxia in rat brain". NMR in Biomedicine 10 2 (1997): 59-66.
http://www.scopus.com/inward/record.url?eid=2-s2.0-0030749195&partnerID=MN8TOARS.
10.1002/(SICI)1099-1492(199704)10:2<59::AID-NBM415>3.0.CO;2-0
- Jones, R.A.; Haraldseth, O.; Baptista, A.M.; Müller, T.B.; Øksendal, A.N.. "A study of the contribution of changes in the
cerebral blood volume to the haemodynamic response to anoxia in rat brain". NMR in Biomedicine 9 6 (1996): 233-240.
http://www.scopus.com/inward/record.url?eid=2-s2.0-0030235961&partnerID=MN8TOARS.
- Jones, R.A.; Müller, T.B.; Haraldseth, O.; Baptista, A.M.; Øksendal, A.N.. "Cerebrovascular changes in rats during ischemia
and reperfusion: A comparison of BOLD and first pass bolus tracking techniques". Magnetic Resonance in Medicine 35
4 (1996): 489-496. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029879652&partnerID=MN8TOARS.
- Anthonsen, H.W.; Baptista, A.; Drabløs, F.; Martel, P.; Petersen, S.B.; Sebastião, M.; Vaz, L.. "Lipases and esterases: a
review of their sequences, structure and evolution.". Biotechnology annual review 1 (1995): 315-371. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029418050&partnerID=MN8TOARS.
10.1016/S1387-2656(08)70056-5
- Anthonsen, H.W.; Baptista, A.; Drabløs, F.; Martel, P.; Petersen, S.B.. "The blind watchmaker and rational protein engineering".
Journal of Biotechnology 36 3 (1994): 185-220. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028031316&partnerID=MN8TOARS.
10.1016/0168-1656(94)90152-X
- Pires, M.J.; Martel, P.; Baptista, A.; Petersen, S.B.; Willson, R.C.; Cabral, J.M.S.. "Improving protein extraction yield
in reversed micellar systems through surface charge engineering". Biotechnology and Bioengineering 44 7 (1994): 773-780.
http://www.scopus.com/inward/record.url?eid=2-s2.0-0028501097&partnerID=MN8TOARS.
|
Poster em conferência |
- Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "pH gradients in
continuum electrostatics calculations of Ccox". Trabalho apresentado em EJIBCE 2014 (2nd Encontro de Jovens Investigadores
de Biologia Estrutural Computacional), Coimbra, Portugal, 2014.
- Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Continuum electrostatics
calculations of Ccox in the presence of a pH gradient". Trabalho apresentado em Protein Electrostatics Satellite Meeting
of EBEC 2014, Lisboa, Portugal, 2014.
- Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Titration of key
sites in bacteriorhodopsin in the presence of a pH gradient". Trabalho apresentado em Frontiers in dynamics simulations
of biological molecules, Barcelona, Spain, 2013.
- Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Probing energy
transduction mechanisms in bacteriorhodopsin using electrostatic calculations". Trabalho apresentado em EBSA 2013 (9th
European Biophysics Congress), Lisboa, Portugal, 2013.
- Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Continuum electrostatics
study of energy transduction mechanisms in bacteriorhodopsin". Trabalho apresentado em COST Action CM0902 Training School
on Molecular machineries for ion translocation across membranes, Lisboa, Portugal, 2013.
- Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "The effect of pH on the interaction between the neuropeptide
kyotorphin and a lipid bilayer: a molecular simulation study". Trabalho apresentado em X Girona Seminar on Theoretical
and Computational Chemistry for the Modeling of Biochemical Systems: From Theory to Applications, Girona, Spain, 2012.
- Baptista, António M.; Magalhães, Pedro R.; Campos, Sara R. R.; Machuqueiro, Miguel. "Ionization of a neuropeptide unaffected
by the membrane environment: simulations of kyotorphin using constant-pH MD and linear response approximation". Trabalho apresentado
em Gordon Research Conference on Protons & Membrane Reactions, San Francisco, USA, 2012.
- Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Simulation of explicit bilayers with constant-pH molecular
dynamics". Trabalho apresentado em 5th Theoretical Biophysics International Symposium, Madeira, Portugal, 2011.
- Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of the neuropeptide
kyotorphin in a lipid bilayer". Trabalho apresentado em Frontiers in Protein Research Interbio Symposium, Oeiras, Portugal,
2011.
- Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of explicit membranes:
study of peptide-bilayer interactions". Trabalho apresentado em V Spanish-Portuguese Biophysics Congress, Zaragoza, Spain,
2010.
|