Manuscripts should be organized in the following way, although papers prepared otherwise will be considered if there are clear and compelling reasons for variation. If authors choose an alternate order, justification for doing so must be included in the cover letter. All manuscript pages must be consecutively numbered.

1. Title page. The title should be concise and informative, but should avoid the use of acronyms and abbreviations. Include (a) full article title; (b) names and affiliations of all authors (matched by superscript numbers); (c) name, mailing address, telephone number, fax number, and E-mail address of the corresponding author; (d) running title of 50 characters or less; (e) list of total number of manuscript pages, supplementary material pages, tables, and figures; and (f) (for submissions made by post) a note indicating that a diskette of the manuscript is included, and what environment and word processor are used; and (g) a description of supplementary material intended for publication in the Electronic Edition, including filenames.

2. Abstract and keywords. Include (a) an abstract of no more than 250 words, followed by (b) four to eight keywords or short phrases for indexing that reflect the content and major thrust of the paper. The abstract should succinctly describe the objectives of the research, the experimental approach, and the major results and their significance. It must be self-explanatory and suitable for abstracting services such as Chemical Abstracts, Biosis, etc. Reference citations in the abstract should be avoided whenever possible and, if necessary, given in full. Avoid the use of abbreviations and acronyms in the abstract unless they are defined therein.

3. Abbreviations and symbols. Use standard abbreviations and acronyms and clearly define uncommon ones parenthetically within the text upon first appearance. The journal will accept standard Journal of Biological Chemistry abbreviations. If abbreviations are particularly complex or numerous, they may be collected into an abbreviations footnote, which will appear on the first or second page of the printed article. Greek symbols should be inserted directly from Word's "symbol insert" pulldown menu; equations/schemes should be inserted using MathType or Word's Equation Editor.

4. Introduction (no heading). The text of the paper begins on a new page. The Introduction should state the purpose of the investigation, the hypotheses tested, and the relationship to other work in the field. Avoid lengthy reviews of the literature.

5. Results. The results should be presented in a clear and concise manner, mentioning figures and tables that summarize or illustrate important findings.

6. Discussion. Briefly interpret the results and relate them to existing knowledge in the field, but do not merely restate the results or present reviews of the literature.

7. Materials and methods. Describe materials and methods briefly but in sufficient detail to allow others to repeat the experiments. Novel procedures should be described in detail, but published procedures should be referenced by a literature citation. If hazardous materials or dangerous procedures are employed, necessary precautions must be stated.

8. Electronic supplementary material. Describe briefly the supplementary material submitted on the diskette with the manuscript that is intended to be available over the Internet as part of the Electronic Edition of Protein Science. The names of all files should be given so that World Wide Web hyperlinks to them can be established within the Electronic Edition. All files provided must conform to the instructions in Section 16.

9. Acknowledgments. Research grants or other funding (including grant or project numbers as appropriate) may be acknowledged, as may significant contributions of individuals providing scholarly, technical, or clerical assistance.

10. References. Authors are asked to avoid extensive references. Protein Science uses the author-date reference style, with in-text citations within parentheses (Hecht 1990--this citation style when there is just one author; Hecht and Smith 1990--this style when there are no more than two authors; OR Hecht et al. 1990--this style when there are three or more authors) and a reference list alphabetized by first author surname (NOT numbered). Surnames and initials of all authors (ONLY use "et al." after 10 authors) and editors of cited works must be provided. All references cited in the text must be included in the References section and vice versa. Titles of journal articles and book chapters must be included; journal titles are abbreviated according to Chemical Abstracts Service Source Index, 1985. Page numbers must be inclusive. If a pre-existing coordinate set is used either in the research or to produce a figure, its databank file code should be given either in the caption or the Materials and Methods section, in addition to whatever literature references may be appropriate.

Please prepare the References list according to the following examples. Note especially:
(a) the punctuation of authors (periods are used after initials, comma used between surname and initials and to separate authors);
(b) publication dates not enclosed in parentheses;
(c) titles required for all journal articles and individual book chapters cited;
(d) only initial word and proper nouns capitalized in article, chapter, and book titles;
(e) periods are used after abbreviated journal titles; and
(f) full page ranges are required (not simply beginning page of article).

EXAMPLES:

Journal Articles

Hecht, M.H., Richardson J.S., Richardson D.C., and Ogden R.C. 1990. De novo design, expression, and characterization of Felix: A four-helix bundle protein of native-like sequence. Science 249: 884-891.

Cierpicki, T., Bania, J., and Otlewski, J. 2000. NMR solution structure of Apis mellifera chymotrypsin/cathepsin G inhibitor-1 (AMCI-1): Structural similarity with Ascaris protease inhibitors. Protein Sci. 9: 976-984.

Books and Book Chapters

Fischmann, D.A., Vaughn, K., Weber, F., and Einheber, S. 1991. Myosis binding proteins: Intracellular members of the immunoglobulin super family. In Frontiers of muscle research: Muscle contraction and muscle dystrophy, 2d ed. (eds. E. Ozawa et al.), pp. 211-222. Elsevier, Amsterdam.

Perutz, M. 1990. Mechanisms of cooperativity and allosteric regulation in proteins. Cambridge University Press, Cambridge, UK.
Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Annual Review of Biochemistry, Advances in Protein Chemistry, Methods in Enzymology, and similar works should be cited in serial publications format. Unpublished data and personal communications must be cited as such parenthetically in the text and must not appear in the References section. All citations of personal communications must be certified by letter from the communicating author.

Linking publish-ahead-of-print references. Authors can now have Medline links in their HTML references for citations that have only been published via Publish-Ahead-of-Print. Since Publish-Ahead-of-Print articles have PubMed records and a PubMed ID (PMID) is listed at the bottom of every PubMed record as the citation identifier, an author can include the PMID within their manuscript references to link the P

Wood, CE, Appt SE, Clarkson TB, Franke AA, Lees CJ, Doerge DR, Cline JM. Effects of high-dose soy isoflavones and equol on reproductive tissues in female cynomolgus monkeys. PMID: 16723506 produces the following:

Wood CE, Appt SE, Clarkson TB, Franke AA, Lees CJ, Doerge DR, Cline JM. Effects of high-dose soy isoflavones and equol on reproductive tissues in female cynomolgus monkeys. PMID: 16723506 [Medline]

11. Tables. All tables must be cited in the text in numerical order and the approximate position of each indicated in the margin. Each table should be typed double-spaced on a separate page (or, if exceptionally large or requiring special symbols or unusual treatment, the table should be submitted camera-ready). Tables should be numbered consecutively with Arabic numerals and grouped together after the References section. A short explanatory title, column headings, and (if necessary) footnotes should make the table intelligible without reference to the text. Vertical and diagonal rules should not be used in tables; instead, indentation and vertical or horizontal space should be used to group data. Large tables of an appendix nature may be considered for electronic publication in the Electronic Edition. If tables are reprinted from another source or if data included are from another source, permission to reprint is required. We cannot use tables produced in Excel at this time. Please produce all tables in your word processing program and save your manuscript whenever possible.

12. Figure legends. Type all figure legends double-spaced. Figure legends should be brief and should not contain methods. Each figure legend must begin with a short statement of the general content of the figure. Symbols indicated in the figure must be identified in the legend text. If figures are reprinted from another source, permission to reprint is required. Explain all symbols and abbreviations.

13. Figures (artwork). Please also read the Electronic Art Submission section. For all manuscripts that are accepted for publication, the authors must mail to the Editorial Office TWO (2) sets of figures as high-quality glossy prints. We also require that authors provide electronic copies of the figures with the manuscript (in .TIFF, .EPS, .GIF, or .JPEG format); this enables the staff to more quickly enter the manuscript into our online system and will expedite the conversion process. Electronic figures and hard copies of figures should be the exact same size and note that for digital artwork to be used for print publication, only .TIFF and .EPS files can be used (reflective art must also accompany the final digital artwork provided for print; see the Electronic Art Submission section). For the best reproduction, halftones should be high contrast. Line drawings, graphs, charts, and chemical formulae should be professionally prepared and labeled. Indicate magnification with a bar scale. Multipart figures should be submitted as one composite.

Label the back of each hard-copy figure with the first author's name, figure number, and an indication of "top". (Electronic copies should be labeled with the first authors name and the figure number, for example Smith_Fig1). Number figures consecutively in the order in which they are referred to in the text. The figure sizes will be adjusted to fit the journal format; therefore, please keep labels, symbols, and other callout devices in proportion to the figure size and detail.

Figures should be kept to the minimum necessary to document results or methods that cannot be described in the text. Linear plots, particularly reciprocal velocity plots, should be avoided and replaced in the text in terms of slopes, intercepts, and standard deviations. All figures must be cited in the text in numerical order and the approximate position of each indicated in the margin. All figures must be camera-ready and have a professional appearance. Most figures will be published in a single column of the Journal; use lettering of sufficient size to be legible after reduction (i.e., labels should be no smaller than 1.5�2 mm high in the reduced figure). Lettering of all figures within the article should be of uniform style (preferably a sans serif typeface; typewritten labels are strongly discouraged). Use uppercase letters A, B, C, etc. to identify individual parts of multipart figures. Poor-quality figures or illegible labeling may result in delayed acceptance and publication.

Check figures carefully before submission to be sure that proper versions are being sent and that there are no labeling errors. Each figure must be clearly identified (on the reverse) by author, article title, (Arabic) figure number, and an indication of the top of the figure. The figures should ordinarily not exceed 8-1/2 X 11" or A4 paper size and must be enclosed in a protective envelope. Submit all original illustrations in duplicate.

Stereo pairs must be mounted side by side. Corresponding points of the two images should be 6.3 cm apart. Please indicate on the label that the figure is a "stereo image."

The use of color is encouraged and justified when it significantly enhances communication and the understanding of the scientific data reported in the original manuscript. Note: Authors can save considerable costs to themselves and the journal by composing Figure 1A, B and C on a single page (or plate) rather than providing these on three separate pages (or plates). For instance, if one figure has three panels and each panel is on a separate page (or plate), then this figure will be counted as three color pages ($350 x 3). To avoid this, provide all three panels on one page (or plate). For best reproduction, bright, clear colors should be used; muted, "muddy" colors produce less satisfactory results. Dark colors against a dark background do not reproduce well. Lemon yellow (especially against a white background) tends to disappear; use slightly greenish or golden yellows instead.

14. Cover artwork. Authors are encouraged to submit a figure, related to their manuscript, that can be considered for use on the cover of the journal. This figure can be included as part of the initial submission, or included when the revised manuscript is being sent back to the Editor following receipt of comments from the referees.

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Manuscript Elements and Order