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					                     ‫טופס- מערך קורס במדרשה לתארים מתקדמים‬
                                                           ‫1. פרטי הקורס‬
       ‫שם הקורס בעברית עקרונות מולקולריים לקשירת מולקולות קטנות לחלבונים‬
 Molecular basis for small molecule interactions with proteins ‫שם הקורס באנגלית‬
                                  ‫שיעור‬        )‫אופן ההוראה בקורס (שיעור, סמינר, שיעור וסמינר‬
        1116.5944.11                       ‫מספר הקורס‬             ‫עברית‬     ‫שפת ההוראה בקורס‬

                                                                         ‫2. שמות מורי הקורס‬
                                                    ‫פרופ' דניאל חננשוילי‬     ‫שם מרכז הקורס‬
                                           ‫שמות המורים המלמדים בקורס פרופ' דניאל חננשוילי‬

                                   )‫3. תכני הקורס (תיאור קצר של המסרים המרכזיים של הקורס‬
Macromolecular interactions of small molecules with proteins are central to most cellular processes.
Experimental methods generate diverse data on these interactions ranging from high throughput
protein-ligand to the crystallised structures of complexes. Despite this, only a fraction of interactions
have been identified and therefore predictive methods are essential to fill in the numerous gaps. Many
predictive methods use information from related proteins. Accordingly, in this course I review different
types of protein domains as related to their conservation of interface and ligand binding sites within
specific protein families. One of the goals of the course is how to identify potential ligand-binding
“pockets” on the protein surface to identify functionally important regulatory sites and potential drug
targets. The relevant approaches may help to characterize newly discovered proteins with unknown
biological and/or biochemical function. The same approaches could be useful for pharmacological
targeting of specific binding sites with a goal of rational development of new drugs. More detailed
syllabus of the course issues is described below.

                                                                              ‫4. היקף הקורס‬
                  24                                               ‫מספר כולל של שעות הקורס‬
            ‫2 שעות שבועיות‬                    )‫פירוט מספר שעות שבועיות ומשך התקופה (סמסטרים‬

                   ‫5. רשימת הנושאים ופירוט השיעורים- כולל שמות המרצים של כל שיעור‬
‫לתשומת ליבכם! בקורס מרובה מורים, על מרכז הקורס לוודא שאין חפיפה בתכנים של‬
                                              .‫השיעורים השונים, וכן שיש קשר הגיוני ביניהם‬
                               .‫נא לפרט את אופן ההוראה בכל שיעור- הרצאה, תרגול, מעבדה‬
   ‫ההוראה‬                                                                         ‫שם‬      '‫מס‬
  ,‫(הרצאה‬                           ‫נושא השיעור‬                                 ‫המרצה‬   ‫שיעור‬
  ‫הרצאה‬    Physico-chemical forces involved in ligand-protein interactions and   ‫דניאל‬   #1
           structural determinants of ligand binding specificity. Structural
           basis for molecular recognition. Major experimental methods for
                ligand-binding assays.
                Protein domain folding and types. Ligand-induced conformational                     #2
                changes in enzymatic catalysis and regulatory signal decoding.
    "—"         Contribution of protein and ligand flexibility in binding energy and   "—"
                entropy loss. Conformational constrain and ligand binding affinity.
    "—"         Protein surface as a major parameter for determining the affinity,
                specificity and selectivity of ligand interactions with proteins.
                Protein “pocket” identification. Anatomy of protein pockets and        "—"
                associated ligands.
    "—"         Domain-domain interactions as a major module for diverging
                protein function and regulatory pathways in the cell. The domain-
                                                                                       "—"          #4
                domain interface and protein function.
"—"   Protein-ligand and protein-protein docking. Screening of small
      molecules and drugs for ligand-protein docking. Experimental and
      computational approaches for identifying new regulatory ligands          "—"    #5
      and rational development of new drugs.

"—"   Domain-ligand Mapping. Ligand binding by single- and multi-
      domains. Domain combinations and substance specificity. Protein-
                                                                               "—"    #6
      ligand interaction databases. Allosteric binding. Structural basis for
      cooperative interactions in oligomeric proteins.
"—"   Time-scales and types of conformational changes in proteins and
      their relevance to protein function. Linker-dependent interactions
                                                                               "—"    #7
      between two domains and hinge-bending conformation transitions.
      CD, NMR, SAXS and FRET techniques for measuring ligand-induced
      conformational changes and interdomain distances.
"—"   Drug-protein interactions. Lipinski’s rules of five. Lead-structure      "—"    #8
      identification and rational development of drugs. Computer-aided
      virtual docking of drug libraries and High Throughput Screening
      (HTS). Robotic synthesis of large libraries of drug-like ligands.
"—"   Protein interactions with lipids. Membrane-embedded protein
      domains. Lipophilic ligands and their interaction with membrane
                                                                               "—"    #9
      proteins. Structural restrictions limiting the selectivity of
      hydrophobic ligand interactions.
"—"   Beyond structural genomics. Advantages and disadvantages of
      computational approaches for the identification of ligand binding
                                                                               "—"    #10
      sites in protein structures. The advantage and restrictions of
      energy-based approaches.
"—"   Types and classes of natural ligand libraries. Why do we need
      natural ligands libraries and how to use them? Why the animal and
                                                                               "—"    #11
      plant toxins have such a high selectivity and affinity for binding to
      specific proteins.
"—"   Evolutionary driving force for reaching highly selective (not
      necessarily high affinity) for ligand binding to proteins. Chemical
                                                                               "—"    #12
      and biological evolution: how they walk together? Perfect enzyme
      catalysts involve diffusion controlled reactions for ligand binding.

                                                                      ‫6. חומר קריאה מאמרים‬

                                                                   ‫7. דרישות קדם לקורס אין‬

                                              ‫8. הגבלת מספר התלמידים בקורס אין הגבלות‬

                                  ‫9. האם הקורס ינתן כל שנה או אחת לשנתיים? כל שנה‬

                                                     ‫11. הרכב הציון הסופי מבחן אמריקאי‬

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