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.
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The discussion section is where you delve into the meaning, importance, and relevance of your results.. It should focus on explaining and evaluating what you found, showing how it relates to your literature review and paper or dissertation topic, and making an argument in support of your overall conclusion.It should not be a second results section.. There are different ways to write this ...
Checklist: Research results 0 / 7. I have completed my data collection and analyzed the results. I have included all results that are relevant to my research questions. I have concisely and objectively reported each result, including relevant descriptive statistics and inferential statistics. I have stated whether each hypothesis was supported ...
Tips to Write the Results Section. Direct the reader to the research data and explain the meaning of the data. Avoid using a repetitive sentence structure to explain a new set of data. Write and highlight important findings in your results. Use the same order as the subheadings of the methods section.
Research results refer to the findings and conclusions derived from a systematic investigation or study conducted to answer a specific question or hypothesis. These results are typically presented in a written report or paper and can include various forms of data such as numerical data, qualitative data, statistics, charts, graphs, and visual aids.
Begin with a clear statement of the principal findings. This will reinforce the main take-away for the reader and set up the rest of the discussion. Explain why the outcomes of your study are important to the reader. Discuss the implications of your findings realistically based on previous literature, highlighting both the strengths and ...
The discussion section is one of the final parts of a research paper, in which an author describes, analyzes, and interprets their findings. They explain the significance of those results and tie everything back to the research question(s). In this handout, you will find a description of what a discussion section does, explanations of how to ...
Reporting Research Results in APA Style | Tips & Examples. Published on December 21, 2020 by Pritha Bhandari.Revised on January 17, 2024. The results section of a quantitative research paper is where you summarize your data and report the findings of any relevant statistical analyses.. The APA manual provides rigorous guidelines for what to report in quantitative research papers in the fields ...
The discussion section provides an analysis and interpretation of the findings, compares them with previous studies, identifies limitations, and suggests future directions for research. This section combines information from the preceding parts of your paper into a coherent story. By this point, the reader already knows why you did your study ...
Papers usually end with a concluding section, often called the "Discussion.". The Discussion is your opportunity to evaluate and interpret the results of your study or paper, draw inferences and conclusions from it, and communicate its contributions to science and/or society. Use the present tense when writing the Discussion section.
II. The Content. The content of the discussion section of your paper most often includes:. Explanation of results: Comment on whether or not the results were expected for each set of findings; go into greater depth to explain findings that were unexpected or especially profound.If appropriate, note any unusual or unanticipated patterns or trends that emerged from your results and explain their ...
Remember, unlike the results section, the discussion ideally focuses on locating your findings in the larger body of existing research. Hence, compare your results with those of other peer-reviewed papers. Example: Although Miller et al. (2020) found evidence of such political bias in a multicultural population, our findings suggest that the ...
An example of research summary in discussion. 3.2. An example of result interpretation in discussion. 3.3. An example of literature comparison in discussion. 3.4. An example of research implications in discussion. 3.5. An example of limitations in discussion.
The results section of a research paper tells the reader what you found, while the discussion section tells the reader what your findings mean. The results section should present the facts in an academic and unbiased manner, avoiding any attempt at analyzing or interpreting the data. Think of the results section as setting the stage for the ...
Discussion is mainly the section in a research paper that makes the readers understand the exact meaning of the results achieved in a study by exploring the significant points of the research, its ...
For example, you may have noticed an unusual correlation between two variables during the analysis of your findings. It is appropriate to highlight this finding in the results section. However, speculating as to why this correlation exists and offering a hypothesis about what may be happening belongs in the discussion section of your paper.
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Below are helpful tips for writing the results and discussion section of a research paper: Please don't repeat the results in the discussion; start with repeating the research questions and explain how the results answer them. Start from the simple results to the complex; you can even start with the conclusion first, but ensure it is ...
By Charlesworth Author Services. In the results section of your academic paper, you present what you found when you conducted your analyses, whereas in your discussion section you explain what your results mean and connect them to prior research studies. In other words, the results section is where you describe what you did, and the discussion ...
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Summarise your results in the text, drawing on the figures and tables to illustrate your points. The text and figures should be complementary, not repeat the same information. You should refer to every table or figure in the text. Any that you don't feel the need to refer to can safely be moved to an appendix, or even removed.
The discussion section of a research paper is where the author analyzes and explains the importance of the study's results. It presents the conclusions drawn from the study, compares them to previous research, and addresses any potential limitations or weaknesses. The discussion section should also suggest areas for future research.
An abstract in research papers is a keyword-rich summary usually not exceeding 200-350 words. It can be considered the "face" of research papers because it creates an initial impression on the readers. While searching databases (such as PubMed) for research papers, a title is usually the first selection criterion for readers.
1. Introduction. Tryptophan (Trp) is the largest amino acid, with important functional roles in proteins. It is often found at protein-protein interfaces, such as antibody-antigen interfaces, accounting for tight interactions and specificity (Samanta & Chakrabarti, 2001), and is ubiquitous in the ligand/substrate-binding sites of, for example, lectins and various enzymes (Zhang et al ...