3. results and discussion, 4. conclusions, 5. related literature, supporting information.
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STRUCTURAL BIOLOGY |
a Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908-0736, USA, and b Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA * Correspondence e-mail: [email protected]
Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the N ɛ —H group, which is a potent donor in canonical hydrogen bonds, and a polarized C δ 1 —H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C—H⋯O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C—H group. Consequently, C α —H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the C ɛ 1 —H and C δ 2 —H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β -sheets. However, the nature and the functional role of interactions involving the C δ 1 —H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution ( r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the C δ 1 —H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5–3.0 kcal mol −1 , depending on the specific stereochemistry.
Keywords: tryptophan ; hydrogen bonds ; C—H⋯O bonds ; protein structure .
The four conformational dihedral angles defining the structure of a tryptophan residue within a polypeptide. |
The resulting database of close contacts had another layer of redundancy due to the presence of noncrystallographic symmetry, which includes biologically relevant oligomers. To eliminate multiple observations of the same contact, we arbitrarily selected the median interaction from oligomeric structures. We assumed that at 1.5 Å resolution or higher, differences between monomers may be due to genuine differences in crystal packing, and so averaging would not be appropriate. However, as the shortest distances might be encumbered by errors, the median contact might be more representative. This final nonredundant data set was used for further calculations of stereochemistry.
3.1. identification of interactions involving trp c δ 1 —h as the donor group.
We obtained 17 012 close contacts, 5983 of which were with water O atoms. Another 1046 contacts involved Glu and Asp carboxylate groups and 1010 contacts were with side-chain hydroxyl groups of Ser, Thr and Tyr. A further 542 contacts involved side-chain carbonyl groups of Asn and Gln. Interestingly, nearly half of all contacts, i.e. 8431 (49.6%), were with backbone carbonyl O atoms, which are particularly strong acceptors owing to their partial negative charge. Given the preponderance of these interactions, we focused on this group of contacts and analysed the respective stereochemistry in order to assess their character and potential function.
The stereochemical parameters used in this study. , and τ are given in ångströms and all angles are given in degrees. |
Left: a histogram of the number of interactions of C 1—H with backbone carbonyl O atoms as a function of the distance (green bars) and a mean value of the α angle in each group, corrected with cubic interpolation. Right: the same statistics for interactions with water molecules. |
Distribution of side-chain dihedral angles for Trp residues involved in contacts with all main-chain carbonyl O atoms. Blue outlines indicate the most populous, low-energy clusters found in proteins, green shows energetically favourable but less common clusters and red represents theoretically unfavourable conformations. |
A histogram showing the number of contacts between C 1—H as a donor and the th main-chain carbonyl O atom as the acceptor. For example, −2 denotes an acceptor located two peptide units upstream in the sequence. |
All calculations up to this point were carried out using raw coordinates from the Protein Data Bank (except for the riding hydrogen positions, which were added independently). As we embarked on the detailed analysis of specific structures, we were concerned about inconsistencies inherent in the data sets in the PDB introduced by different protocols or refinement and different software. Specifically, we were concerned about the lack of inclusion of H atoms during refinement, the lack of coordinates in the file etc . To avoid bias, all structures described below were subjected to additional standardized refinement and addition of riding H atoms at correct, uniform positions using the PyMOL script. Details are described in the supporting information and Supplementary Table S1 .
A double scatter plot (Ramachandran φ/ψ, blue; conformational, χ /χ , red) for Trp residues in all structural motifs in the +1 class. The clusters are identified by type as shown in Fig. 4 . |
Examples of the three conformational Trp clusters in the +1 class. ( ) 90 (PDB entry ; only the C atom of Trp178 is shown for clarity), ( ) 0 (PDB entry ), ( ) -105 (PDB entry ). |
Class −1 of interactions. ( ) A double scatter plot (Ramachandran φ/ψ, blue; conformational, χ /χ , red) for Trp residues in all motifs. ( ) An example from the 0 cluster (PDB entry ; only the C atom of Trp43 is shown for clarity). |
A small minority of contacts in this class, i.e. 30 examples, are of the m 105 type and almost all involve Trp residues in the α L region of the Ramachandran plot, with long d HO distances. Such stereochemistry suggests weak interactions. There are only three structures in the p -90 cluster.
The −2 class of interactions. A double scatter plot (Ramachandran φ/ψ, blue; conformational, χ /χ , red) for Trp residues in all structural motifs identified in this class. |
The m 0 cluster is represented by 190 structures. It is very close in conformational space to m 105 because the m 105 structures are shifted to lower χ 2 , with an average value of 82°, while the m 0 cluster is also shifted to higher values of χ 2 , with an average of 23°. In both groups Trp is primarily found in extended, β -secondary conformations, although right-handed and left-handed helical structures are also observed.
Examples of the three conformational Trp clusters in the +2 class. ( ) 0 (PDB entry ; only the C atoms of non-Trp residues are shown for clarity), ( ) 105 (PDB entry ), ( ) -90 (PDB entry ). |
Of note is the fact that many of the motifs in all three clusters resemble the classic type II β -turn. The conformation of Trp is such that the C δ 1 —H group mimics the peptide amide which would serve as a donor in a classical β -turn, adding just one atom to the turn (11 atoms instead of 10). Therefore, the direction of the hydrogen bond is preserved, with residue i donating the hydrogen bond to residue i − 2. Unlike the canonical β -turn, this structural feature does not reverse the direction of the polypeptide chain but creates kinks and turns of ∼110°.
The −3 class of interactions. A double scatter plot (Ramachandran φ/ψ, blue; conformational, χ /χ , red) for Trp residues in all structural motifs in this class. |
The m 105 cluster contains motifs with Trp found in both α and β secondary structures. The average α H is 137.9°, but α O is again unfavourable (average 113.8°). Except for a few outliers, the p -90 cluster is stereochemically tight, with a mean χ 1 of 66° and χ 2 of −89°. The vast majority of the motifs contain Trp in an α -helical form, and the putative hydrogen bond has a more favourable geometry, with an α H of 138.5° and an α O of 135.4°, with an average elevation of 0.6 Å on the si face. The small m 0 cluster contains several motifs with Trp in α , β and left-handed helical secondary conformations. The d HO distances are longer in this cluster, with an average α H of 140.7° and α O of 136.4°
Examples of the three conformational Trp clusters in the +3 class. ( ) 0 (PDB entry ; only the C atoms of non-Trp residues are shown for clarity), ( ) 105 (PDB entry ), ( ) -90 (PDB entry ). Note that ( ) and ( ) contain three-centred hydrogen bonds from the C 1—H and amide groups to the − 3 carbonyl reminiscent of a 3 -helical hydrogen-bonding pattern (canonical amide-to-carbonyl hydrogen bonds are shown as fine dashed lines). |
The −4 class of interactions. A double scatter plot (Ramachandran φ/ψ, blue; conformational, χ /χ , red) for Trp residues in all structural motifs in this class. |
Examples of the three conformational Trp clusters in the +4 class. ( ) 0 (PDB entry ; only the C atoms of non-Trp residues are shown for clarity, ( ) 105 (PDB entry ), ( ) -90 (PDB entry ). Note that all motifs contain hydrogen bonds from the C 1—H and amide groups to the − 4 carbonyl, capping it with a three-centred bond. |
The rare m 0 motifs also contain Trp in both α and β secondary conformations. They tend to have an unfavourable angular stereochemistry, with an average α H of 128° and α O of 141°, and longer d HO distances.
All interactions show cohesive E int values irrespective of stereochemistry. As expected, the weakest E int values were obtained for those interactions in which the H atom is located significantly out of the sp 2 plane of the acceptor O atom. It appears that the α H and α O angles are less of a factor: both can be as low as ∼130° without a significant reduction in E int , as long as the hydrogen is within ∼0.8 Å of the sp 2 plane. We also noted that many of the structural motifs that we investigated show d HO distances as short as ∼2.0 Å, significantly shorter than the predicted optimal distance of ∼2.3 Å. We wondered whether such short interactions, resulting from intramolecular constraints, might be less favourable.
We also present evidence based on quantum-chemical calculations that the short C δ 1 —H⋯O=C contacts revealed by structural data mining are in fact invariably cohesive interactions of the order of approximately half a canonical hydrogen bond, and less sensitive to specific stereochemistry, such as C—H⋯O and H⋯O=C angles, than previously thought. The critical factor is the position of the H atom close to the sp 2 plane of the acceptor O atom. Note on the precision of the crystallographic coordinates and Supplementary Methods. DOI: https://doi.org/10.1107/S2059798324005515/chr5002sup1.pdf Supplementary Table S1. Crystallographic re-refinement of structural models analysed in the paper. DOI: https://doi.org/10.1107/S2059798324005515/chr5002sup2.xlsx ‡ Current address: Department of Biochemistry, Biophysics and Biotechnology, Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland. AcknowledgementsThe authors declare no competing financial interests. Funding informationZSD and WM are supported by Harrison Family Funds; WM and ZSD acknowledge National Institutes of Health grants GM132595 and GM086457, respectively. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence , which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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The serotonin hypothesis of depression is still influential. We aimed to synthesise and evaluate evidence on whether depression is associated with lowered serotonin concentration or activity in a ...
The serotonin hypothesis of depression is still influential. We aimed to synthesise and evaluate evidence on whether depression is associated with lowered serotonin concentration or activity in a systematic umbrella review of the principal relevant areas of research. ... and methods to reduce serotonin availability using tryptophan depletion do ...
The "serotonin hypothesis" of clinical depression is almost 50 years old. At its simplest, the hypothesis proposes that diminished activity of serotonin pathways plays a causal role in the pathophysiology of depression. ... In healthy participants with no risk factors for depression, tryptophan depletion does not produce clinically ...
Nonetheless, tryptophan depletion offers a straightforward way to test the serotonin hypothesis of depression. It is well established that tryptophan depletion in healthy participants, who lack obvious risk factors for depression, does not cause significant lowering of mood ( Ruhé et al., 2007 ).
The serotonin hypothesis of depression is still influential. We aimed to synthesise and evaluate evidence on whether depression is associated with lowered serotonin concentration or activity in a systematic umbrella review of the principal relevant areas of research. ... (SERT) levels measured by imaging or at post-mortem; tryptophan depletion ...
Nonetheless, tryptophan depletion offers a straightforward way to test the serotonin hypothesis of depression. It is well established that tryptophan depletion in healthy participants, who lack obvious risk factors for depression, does not cause significant lowering of mood ( Ruhé et al., 2007 ).
The main areas of research do not provide support for the most well-known neurochemical hypothesis, the serotonin theory of depression—the idea that depression is caused by low levels or low ...
Keywords. Serotonin, depression, psychopharmacology, learning, positron emission tomography. The notion that clinical depression might be caused by deficient activity of the brain neurotransmitter, serotonin (5-hydroxy-tryptamine (5-HT)) is over 50 years old. This theory seems to have been first proposed in 1967 by the British psychiatrist ...
The serotonin hypothesis of depression is still influential. We aimed to synthesise and evaluate evidence on whether depression is associated with lowered serotonin concentration or activity in a systematic umbrella review of the principal relevant areas of research. PubMed, EMBASE and PsycINFO were searched using terms appropriate to each area of research, from their inception until December ...
Antidepressants remain an effective treatment for depression, even without the "chemical imbalance" explanation. A recent umbrella review of evidence for the serotonin theory of depression 1 was widely reported in UK media as showing that depression is not caused by low levels of serotonin or a "chemical imbalance" and therefore casting ...
One important player in depression is the amino acid tryptophan. This amino acid can be metabolized in two important pathways in the context of depression: the serotonin and kynurenine pathways. These metabolic pathways of tryptophan are crucial in several processes that are linked with depression. Indeed, the maintenance of the balance of ...
Tryptophan depletion is a widely used paradigm to study serotonin system-related mechanisms in the pathophysiology and treatment of depression. There is convincing evidence that tryptophan depletion primarily and selectively affects serotonergic transmission. The behavioral data in healthy controls with and without genetic risk for depression ...
Due in part to the effectiveness of selective serotonin reuptake inhibitors (SSRIs) in the ... whereas perturbation of the serotonin system using tryptophan depletion influenced . 8 resting-state activity in the amygdala, ... Given the neurotrophin hypothesis of depression, as well as data implicating ELS as a vulnerability marker for MDD (Gatt ...
It has been found that dietary intake of tryptophan can modulate central nervous system concentrations of serotonin in humans, and that tryptophan depletion aggravates depression. Figure 6. Tryptophan, its metabolites, and lactic acid produced by the gut microbiome ... For more on how emerging trends and new approaches are helping the millions ...
The serotonin (5-HT) hypothesis of depression dates from the 1960s. It originally postulated that a deficit in brain serotonin, corrected by antidepressant drugs, was the origin of the illness. ... Animal models as described earlier have shown that modifying any of the components of the 5-HT system, including tryptophan hydroxylase, ...
Restriction of dietary l-tryptophan (which is required for 5-HT synthesis) impairs short-term and long-term memory in rodents and humans (1, 2). In addition, depletion of 5-HT during synaptogenesis (using a tryptophan hydroxylase inhibitor) decreases synaptic density in the adult rat hippocampus .
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The serotonin hypothesis of depression is still influential. We aimed to synthesise and evaluate evidence on whether depression is. ... review of tryptophan depletion studies has been performed since 2007. The two largest and highest quality studies of the SERT. gene, one genetic association study (n = 115,257) and one collaborative meta ...
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Results Distinct shifts in taxonomic and functional profiles of gut microbiota and their related metabolites were observed in different IA stages. Notably, tryptophan metabolites, particularly indoxyl sulfate (IS), were significantly higher in plasma of RIA. Meanwhile, upregulated tryptophanase expression and indole-producing microbiota were observed in gut microbiome of RIA.
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There is a high need for the development of new therapies and gaining new insights into this disease is urgent. One important player in depression is the amino acid tryptophan. This amino acid can be metabolized in two important pathways in the context of depression: the serotonin and kynurenine pathways.
Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the N ɛ —H group, which is a potent donor in canonical hydrogen bonds, and a polarized C δ 1 —H group, which is capable of forming weaker, noncanonical hydrogen bonds.
Tryptophan helps the body produce serotonin, a neurotransmitter that regulates behavior, mood, memory and digestion, according to the National Institutes of Health online library of medicine.
The serotonin hypothesis of depression is still influential. We aimed to synthesise and evaluate evidence on whether depression is ... tryptophan depletion (which lowers available serotonin) can ...