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Solvation properties of proteins in membranes
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Knowledge about the insertion and stabilization of membrane proteins is a key step towards understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic to insert efficiently, but there are many exceptions with unfavorable polar or titratable residues. Since evolutionary conserved these amino acids are likely of paramount functional importance, e.g. the four arginines in the S4 voltage sensor helix of voltage-gated ion channels. This has lead to vivid discussion about their conformation, protonation state and cost of insertion. To address such questions, the main focus of this thesis has been membrane protein solvation in lipid bilayers, evaluated using molecular dynamics simulations methods.

A main result is that polar and charged amino acids tend to deform the bilayer by pulling water/head-groups into the hydrophobic core to keep their hydrogen bonds paired, thus demonstrating the adaptiveness of the membrane to allow specific and quite complex solvation. In addition, this retained hydration suggests that the solvation cost is mainly due to entropy, not enthalpy loss. To further quantify solvation properties, free energy profiles were calculated for all amino acids in pure bilayers, with shapes correlating well with experimental in vivo values but with higher magnitudes. Additional profiles were calculated for different protonation states of the titratable amino acids, varying lipid composition and with transmembrane helices present in the bilayer. While the two first both influence solvation properties, the latter seems to be a critical aspect. When the protein fraction in the models resemble biological membranes, the solvation cost drops significantly - even to values compatible with experiment.

In conclusion, by using simulation based methods I have been able to provide atomic scale explanations to experimental results, and in particular present a hypothesis for how the solvation of charged groups occurs.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University , 2009. , 62 p.
Keyword [en]
membrane protein, lipid bilayer, free energy, solvation, insertion, molecular dynamics simulations, protein mass fraction
National Category
Theoretical Chemistry
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-27437ISBN: 978-91-7155-856-5 (print)OAI: oai:DiVA.org:su-27437DiVA: diva2:214204
Public defence
2009-06-12, Magnelisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12, Stockholm, 13:00 (English)
Opponent
Supervisors
Available from: 2009-05-22 Created: 2009-05-04 Last updated: 2013-07-09Bibliographically approved
List of papers
1. Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
Open this publication in new window or tab >>Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
2008 (English)In: Proteins: Structure, Function, and Genetics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 70, no 4, 1332-1344 p.Article in journal (Refereed) Published
Keyword
Amino Acids/*chemistry, Computer Simulation, Lipid Bilayers, Membrane Proteins, Models; Molecular, Motion, Solubility, Thermodynamics
Identifiers
urn:nbn:se:su:diva-17305 (URN)10.1002/prot.21629 (DOI)000253567400023 ()17876818 (PubMedID)
Available from: 2009-01-23 Created: 2009-01-23 Last updated: 2017-12-13Bibliographically approved
2. Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations
Open this publication in new window or tab >>Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations
2006 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 91, no 12, 4450-4463 p.Article in journal (Refereed) Published
Keyword
Amino Acids/*chemistry, Cell Membrane, Computer Simulation, Hydrogen Bonding, Membrane Proteins/*chemistry, Models; Molecular, Protein Folding, Protein Structure; Secondary, Water/chemistry
Identifiers
urn:nbn:se:su:diva-11255 (URN)10.1529/biophysj.106.092767 (DOI)17012325 (PubMedID)
Available from: 2008-01-10 Created: 2008-01-10 Last updated: 2017-12-13Bibliographically approved
3. Titratable amino acid solvation in lipid membranes as a function of protonation state
Open this publication in new window or tab >>Titratable amino acid solvation in lipid membranes as a function of protonation state
2009 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 1, 245-253 p.Article in journal (Refereed) Published
Abstract [en]

Knowledge about the insertion and stabilization of membrane proteins is a key step toward understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic so as to efficiently insert into membranes, but there are many exceptions with polar or titratable residues. An obvious example is the S4 helices of voltage-gated ion channels with up to 4 arginines, leading to vivid discussion about whether such helices can insert spontaneously, and if so, what their conformation, protonation state, and cost of insertion really are. To address this question, we have determined geometric and energetic solvation properties for different protonation states of the titrateable amino acids, including hydration, side chain orientation, free energy profiles, and effects on the membrane thickness. As expected, charged states are significantly more expensive to insert (8-16 kcal/mol) than neutral variants (1-3 kcal/mol). Although both sets of values exhibit quite high relative correlation with experimental in vivo hydrophobicity scales, the magnitudes of the in vivo hydrophobicity scales are much lower and strikingly appears as a compressed version of the calculated values. This agrees well with computational studies on longer lipids but results in an obvious paradox: the differences between in vivo insertion and simulations cannot be explained by methodological differences in force fields, possible limited hydrophobic thickness of the endoplasmic reticulum (ER) membrane, or parameters; even anionic lipid head groups (PG) only have limited effect on charged side chains, and virtually none for hydrophobic ones. This leads us to propose a model for in vivo insertion that could reconcile these differences and explain the correlation: if there are considerable hydrophobic barriers inside the translocon, the experimental reference state for the solvation free energy when comparing insertion/translocation in vivo would be quite close to the bilayer environment rather than water.

Identifiers
urn:nbn:se:su:diva-27089 (URN)10.1021/jp8048873 (DOI)000262167800031 ()19118487 (PubMedID)
Available from: 2009-04-22 Created: 2009-04-22 Last updated: 2017-12-13Bibliographically approved
4. The role of lipid composition for insertion and stabilization of amino acids in membranes
Open this publication in new window or tab >>The role of lipid composition for insertion and stabilization of amino acids in membranes
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 18, 185101- p.Article in journal (Refereed) Published
Abstract [en]

While most membrane protein helices are clearly hydrophobic, recent experiments have indicated that it is possible to insert marginally hydrophobic helices into bilayers and have suggested apparent in vivo free energies of insertion for charged residues that are low, e.g., a few kcals for arginine. In contrast, a number of biophysical simulation studies have predicted that the bilayer interior is close to a pure hydrophobic environment with large penalties for hydrophilic amino acids--and yet the experimental scales do significantly better at predicting actual membrane proteins from sequence. Here, we have systematically studied the dependence of the free energy profiles on lipid properties, including tail length, saturation, headgroup hydrogen bond strength, and charge, both to see to whether the in vivo insertion can be explained in whole or part from lipid composition of the endoplasmic reticulum (ER) membranes, and if the solvation properties can help interpret how protein function depends on the lipids. We find that lipid charge is important to stabilize charged amino acids inside the bilayer (with implications, e.g., for ion channels), that thicker bilayers have higher solvation costs for hydrophilic side chains, and that headgroup hydrogen bond strength determines how adaptive the lipids are as a hydrophobic/hydrophilic solvent. None of the different free energy profiles are even close to the low apparent in vivo insertion cost, which suggests that regardless of the specific ER membrane composition the current experimental results cannot be explained by normal lipid-type variation.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-34700 (URN)10.1063/1.3129863 (DOI)000266263200054 ()19449954 (PubMedID)
Available from: 2010-01-11 Created: 2010-01-11 Last updated: 2017-12-12Bibliographically approved
5. Protein contents in biological membranes explain abnormal solvation of charged and polar residues
Open this publication in new window or tab >>Protein contents in biological membranes explain abnormal solvation of charged and polar residues
2009 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 37, 15684-15689 p.Article in journal (Refereed) Published
Abstract [en]

Transmembrane helices are generally believed to insert into membranes based on their hydrophobicity. Nevertheless, there are important exceptions where polar or titratable residues have great functional importance, for instance the S4 helix of voltage-gated ion channels. It has been shown experimentally that insertion can be accomplished by hydrophobic counterbalance, which enabled biological hydrophobicity scales that predict an arginine insertion cost of only 2.5 kcal/mol, compared to 14.9 kcal/mol in cyklohexane. Previous simulations of pure bilayers have produced values close to the pure hydrocarbon, which has lead to vivid discussion about the experimental conditions.  Here, we have performed computer simulations of models better mimicking biological membranes by explicitly including protein helices at mass fractions from 15% to 55%. This has a striking effect on the solvation free energy of arginine, which drops more than a factor of two even for purely hydrophobic extra helices. With some polar residues present, the solvation cost comes close to experimental observation around 30% mass fraction, and negligible at 40%. The effect is mainly due to the extra helices making it easier for arginine to retain hydration water, with increasing amounts at higher protein mass fraction. These results offer a possible explanation to the previous discrepancy between the in vivo hydrophobicity scale and computer simulations, and highlight the importance of the relatively high protein contents in biological membranes. While many membrane proteins are stable in pure bilayers, the simplified models might not be sufficiently accurate descriptions of insertion for polar or charged residues in biological membranes.

Keyword
membrane protein, lipid bilayer, protein mass fraction, free energy, solvation, insertion, molecular dynamics simulation
Identifiers
urn:nbn:se:su:diva-27094 (URN)10.1073/pnas.0905394106 (DOI)000269806600034 ()
Available from: 2009-04-22 Created: 2009-04-22 Last updated: 2017-12-13Bibliographically approved

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