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Kamerlin, Shina C. LynnORCID iD iconorcid.org/0000-0002-3190-1173
Alternative names
Publications (10 of 83) Show all publications
Al-Smadi, D., Enugala, T. R., Kessler, V., Mhasal, A. R., Kamerlin, S. C., Kihlberg, J., . . . Widersten, M. (2019). Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di-, and Tri-Hydroxypentanones. Journal of Organic Chemistry, 84(11), 6982-6991
Open this publication in new window or tab >>Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di-, and Tri-Hydroxypentanones
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2019 (English)In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 84, no 11, p. 6982-6991Article in journal (Refereed) Published
Abstract [en]

Polyhydroxylated compounds are building blocks for the synthesis of carbohydrates and other natural products. Their synthesis is mainly achieved by different synthetic versions of aldol-coupling reactions, catalyzed either by organocatalysts, enzymes or metal-organic catalysts. We have investigated the formation of 1,4-substituted 2,3-dihydroxybutan-1-one derivatives from para- and meta-substituted phenylacetaldehydes by three distinctly different strategies. The first involved a direct aldol reaction with hydroxyacetone, dihydroxyacetone or 2-hydroxyacetophenone, catalyzed by the cinchona derivative cinchonine. The second was reductive cross-coupling with methyl or phenyl glyoxal promoted by SmI2 resulting in either 5-substituted 3,4-dihydroxypentan-2-ones or 1,4 bis-phenyl substituted butanones, respectively. Finally, in the third case, aldolase catalysis was employed for synthesis of the corresponding 1,3,4-trihydroxylated pentan-2-one derivatives. The organocatalytic route with cinchonine generated distereomerically enriched syn products (de = 60−99 %), with moderate enantiomeric excesses (ee = 43−56%), but did not produce aldols with either hydroxyacetone or dihydroxyacetone as donor ketones. The SmI2-promoted reductive cross-coupling generated product mixtures with diastereomeric and enantiomeric ratios close to unity. This route allowed for the production of both 1-methyl- and 1-phenylsubstituted 2,3-dihydroxybutanones, at yields between 40−60%. Finally, the biocatalytic approach resulted in enantiopure syn (3R,4S) 1,3,4-trihydroxypentan-2-ones.

National Category
Organic Chemistry
Research subject
Chemistry with specialization in Organic Chemistry
Identifiers
urn:nbn:se:uu:diva-383068 (URN)10.1021/acs.joc.9b00742 (DOI)000471212000043 ()
Available from: 2019-05-08 Created: 2019-05-08 Last updated: 2019-07-05Bibliographically approved
Baier, F., Hong, N., Yang, G., Pabis, A., Miton, C. M., Barrozo, A., . . . Tokuriki, N. (2019). Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes. eLIFE, 8, Article ID e40789.
Open this publication in new window or tab >>Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes
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2019 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 8, article id e40789Article in journal (Refereed) Published
Abstract [en]

Genetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may impact the evolvability of proteins, but the underlying molecular basis remains unclear. Here, we performed comparative directed evolution of four orthologous metallo-beta-lactamases toward a new function and found that different starting genotypes evolved to distinct evolutionary outcomes. Despite a low initial fitness, one ortholog reached a significantly higher fitness plateau than its counterparts, via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show how cryptic molecular properties and conformational variation of active site residues in the initial genotypes cause epistasis, that could lead to distinct evolutionary outcomes. Our work highlights the importance of understanding the molecular details that connect genetic variation to protein function to improve the prediction of protein evolution.

Place, publisher, year, edition, pages
ELIFE SCIENCES PUBLICATIONS LTD, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-378387 (URN)10.7554/eLife.40789 (DOI)000458485100001 ()30719972 (PubMedID)
Available from: 2019-03-05 Created: 2019-03-05 Last updated: 2019-03-05Bibliographically approved
Calixto, A. R., Moreira, C., Pabis, A., Kötting, C., Gerwert, K., Rudack, T. & Kamerlin, S. C. L. (2019). GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. Journal of the American Chemical Society, 141(27), 10684-10701
Open this publication in new window or tab >>GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases
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2019 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 27, p. 10684-10701Article in journal (Refereed) Published
Abstract [en]

GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the G(alpha i), subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-390792 (URN)10.1021/jacs.9b03193 (DOI)000475533500017 ()31199130 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW 2013.0124Stiftelsen Olle Engkvist Byggmästare, 190-0335Wenner-Gren FoundationsGerman Research Foundation (DFG), 321722360
Available from: 2019-08-15 Created: 2019-08-15 Last updated: 2019-08-15Bibliographically approved
Mydy, L. S., Cristobal, J. R., Katigbak, R. D., Bauer, P., Reyes, A. C., Kamerlin, S. C., . . . Gulick, A. M. (2019). Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry, 58(8), 1061-1073
Open this publication in new window or tab >>Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies
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2019 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 58, no 8, p. 1061-1073Article in journal (Refereed) Published
Abstract [en]

Human liver glycerol 3-phosphate dehydrogenase (hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme-substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E.NAD, and ternary E.NAD.DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. These results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-379583 (URN)10.1021/acs.biochem.8b01103 (DOI)000460199700009 ()30640445 (PubMedID)
Funder
Swedish Research Council, 2015-04928
Available from: 2019-03-25 Created: 2019-03-25 Last updated: 2019-03-25Bibliographically approved
Liao, Q., Lüking, M., Krueger, D. M., Deindl, S., Elf, J., Kasson, P. M. & Kamerlin, S. C. (2019). Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition. Journal of Physical Chemistry B, 123(17), 3576-3590
Open this publication in new window or tab >>Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition
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2019 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 17, p. 3576-3590Article in journal (Refereed) Published
Abstract [en]

Recent years have witnessed an explosion of interest in computational studies of DNA binding proteins, including both coarse grained and atomistic simulations of transcription factor-DNA recognition, to understand how these transcription factors recognize their binding sites on the DNA with such exquisite specificity. The present study performs microsecond time scale all-atom simulations of the dimeric form of the lactose repressor (Lad), both in the absence of any DNA and in the presence of both specific and nonspecific complexes, considering three different DNA sequences. We examine, specifically, the conformational differences between specific and nonspecific protein DNA interactions, as well as the behavior of the helix-turn-helix motif of Lad when interacting with the DNA. Our simulations suggest that stable Lad binding occurs primarily to bent A-form DNA, with a loss of Lad conformational entropy and optimization of correlated conformational equilibria across the protein. In addition, binding to the specific operator sequence involves a slightly larger number of stabilizing DNA protein hydrogen bonds (in comparison to nonspecific complexes), which may account for the experimentally observed specificity for this operator. In doing so, our simulations provide a detailed atomistic description of potential structural drivers for LacI selectivity.

National Category
Physical Chemistry Biophysics
Identifiers
urn:nbn:se:uu:diva-384077 (URN)10.1021/acs.jpcb.8b12363 (DOI)000466989000003 ()30952192 (PubMedID)
Funder
Swedish Research Council, 2016-06213Knut and Alice Wallenberg Foundation, KAW 2016.0077
Available from: 2019-05-28 Created: 2019-05-28 Last updated: 2019-05-28Bibliographically approved
Tatum, N. J., Duarte, F., Kamerlin, S. C. L. & Pohl, E. (2019). Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds. Journal of Physical Chemistry Letters, 10(9), 2244-2249
Open this publication in new window or tab >>Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds
2019 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 9, p. 2244-2249Article in journal (Refereed) Published
Abstract [en]

Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were often proposed, though only the top scoring pose was utilized for filtering of the large data set. We obtained biophysically validated hits, some of which yielded complex crystal structures. In some cases, the crystallized binding mode and top scoring mode agree, while for others an alternate ligand binding orientation was found. In this contribution, we combine rigid docking, molecular dynamics simulations, and the linear interaction energy method to calculate binding free energies and derive relative binding energies for a number of EthR inhibitors in both modes. This strategy allowed us to correctly predict the most favorable orientation. Therefore, this widely applicable approach will be suitable to triage multiple binding modes within EthR and other potential drug targets with similar characteristics.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2019
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-383836 (URN)10.1021/acs.jpclett.9b00741 (DOI)000466991300033 ()30965004 (PubMedID)
Funder
The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2019-05-28 Created: 2019-05-28 Last updated: 2019-05-28Bibliographically approved
Parkash, V., Kulkarni, Y., ter Beek, J., Shcherbakova, P. V., Kamerlin, S. C. L. & Johansson, E. (2019). Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon. Nature Communications, 10, Article ID 373.
Open this publication in new window or tab >>Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon
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2019 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 373Article in journal (Refereed) Published
Abstract [en]

The most frequently recurring cancer-associated DNA polymerase epsilon (Pol epsilon) mutation is a P286R substitution in the exonuclease domain. While originally proposed to increase genome instability by disrupting exonucleolytic proofreading, the P286R variant was later found to be significantly more pathogenic than Pol epsilon proofreading deficiency per se. The mechanisms underlying its stronger impact remained unclear. Here we report the crystal structure of the yeast orthologue, Pol epsilon-P301R, complexed with DNA and an incoming dNTP. Structural changes in the protein are confined to the exonuclease domain, with R301 pointing towards the exonuclease site. Molecular dynamics simulations suggest that R301 interferes with DNA binding to the exonuclease site, an outcome not observed with the exonuclease-inactive Pol epsilon-D290A, E292A variant lacking the catalytic residues. These results reveal a distinct mechanism of exonuclease inactivation by the P301R substitution and a likely basis for its dramatically higher mutagenic and tumorigenic effects.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-376827 (URN)10.1038/s41467-018-08114-9 (DOI)000456286400001 ()30670696 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilSwedish Cancer SocietyNIH (National Institute of Health), ES015869
Available from: 2019-02-11 Created: 2019-02-11 Last updated: 2019-02-11Bibliographically approved
Osterlund, N., Kulkarni, Y. S., Misiaszek, A. D., Wallin, C., Krueger, D. M., Liao, Q., . . . Graslund, A. (2018). Amyloid-beta Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects. ACS Chemical Neuroscience, 9(7), 1680-1692
Open this publication in new window or tab >>Amyloid-beta Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects
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2018 (English)In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 9, no 7, p. 1680-1692Article in journal (Refereed) Published
Abstract [en]

The amphiphilic nature of the amyloid-beta (A beta) peptide associated with Alzheimer's disease facilitates various interactions with biomolecules such as lipids and proteins, with effects on both structure and toxicity of the peptide. Here, we investigate these peptide-amphiphile interactions by experimental and computational studies of A beta(1-40) in the presence of surfactants with varying physicochemical properties. Our findings indicate that electrostatic peptide-surfactant interactions are required for coclustering and structure induction in the peptide and that the strength of the interaction depends on the surfactant net charge. Both aggregation-prone peptide-rich coclusters and stable surfactant-rich coclusters can form. Only A beta(1-40) monomers, but not oligomers, are inserted into surfactant micelles in this surfactant-rich state. Surfactant headgroup charge is suggested to be important as electrostatic peptide-surfactant interactions on the micellar surface seems to be an initiating step toward insertion. Thus, no peptide insertion or change in peptide secondary structure is observed using a nonionic surfactant. The hydrophobic peptide-surfactant interactions instead stabilize the A beta monomer, possibly by preventing self-interaction between the peptide core and C terminus, thereby effectively inhibiting the peptide aggregation process. These findings give increased understanding regarding the molecular driving forces for A beta aggregation and the peptide interaction with amphiphilic biomolecules.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
Keywords
Alzheimer's disease, A beta aggregation, surfactant interactions, optical and NMR spectroscopy, mass spectrometry, molecular dynamics simulations
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-386225 (URN)10.1021/acschemneuro.8b00065 (DOI)000439531400017 ()29683649 (PubMedID)
Funder
Swedish Research Council
Available from: 2019-06-19 Created: 2019-06-19 Last updated: 2019-06-19Bibliographically approved
Petrovic, D., Szeler, K. & Kamerlin, S. C. L. (2018). Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chemical Communications, 54(25), 3077-3089
Open this publication in new window or tab >>Challenges and advances in the computational modeling of biological phosphate hydrolysis
2018 (English)In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 25, p. 3077-3089Article, review/survey (Refereed) Published
Abstract [en]

Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer. 

National Category
Theoretical Chemistry
Research subject
Chemistry; Biochemistry
Identifiers
urn:nbn:se:uu:diva-340612 (URN)10.1039/C7CC09504J (DOI)000428845500001 ()29412205 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW 2013.0124
Available from: 2018-02-01 Created: 2018-02-01 Last updated: 2018-08-10Bibliographically approved
Barrozo, A., Liao, Q., Esguerra, M., Marloie, G., Florian, J., Williams, N. H. & Kamerlin, S. C. L. (2018). Computer simulations of the catalytic mechanism of wild-type and mutant beta-phosphoglucomutase. Organic and biomolecular chemistry, 16(12), 2060-2073
Open this publication in new window or tab >>Computer simulations of the catalytic mechanism of wild-type and mutant beta-phosphoglucomutase
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2018 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 16, no 12, p. 2060-2073Article in journal (Refereed) Published
Abstract [en]

beta-Phosphoglucomutase (beta-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of beta-glucose-1-phosphate to -glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity. However, computational studies have suggested that a substrate-assisted mechanism is viable for many phosphotransferases. Therefore, we carried out empirical valence bond (EVB) simulations to address the plausibility of this mechanistic alternative, including its role in the abolished catalytic activity of the D10S, D10C and D10N point mutants of beta-PGM. In addition, we considered both of these mechanisms when performing EVB calculations of the catalysis of the wild type (WT), H20A, H20Q, T16P, K76A, D170A and E169A/D170A protein variants. Our calculated activation free energies confirm that D10 is likely to serve as the general base/acid for the reaction catalyzed by the WT enzyme and all its variants, in which D10 is not chemically altered. Our calculations also suggest that D10 plays a dual role in structural organization and maintaining electrostatic balance in the active site. The correct positioning of this residue in a catalytically competent conformation is provided by a functionally important conformational change in this enzyme and by the extensive network of H-bonding interactions that appear to be exquisitely preorganized for the transition state stabilization.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2018
National Category
Biochemistry and Molecular Biology Organic Chemistry
Identifiers
urn:nbn:se:uu:diva-351705 (URN)10.1039/c8ob00312b (DOI)000428808500007 ()29508879 (PubMedID)
Funder
Swedish Research Council, 2015-04928
Available from: 2018-05-31 Created: 2018-05-31 Last updated: 2018-11-29Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-3190-1173

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