🎬 ON DEMAND VIDEO
Structural Clues to HLA-B Mediated Type 1 Diabetes Risk Ruby Sharma PhD • July 7 2026
📺 Now available on demand ▶ Watch the Full Talk
💬 Key Quote
“Even a single difference in the amino acid change can entirely change the disease spectrum.” — Ruby Sharma, PhD
🔬 Foundational Insights as They Apply to T1D
Most of what the T1D field knows about HLA risk concerns class II molecules — HLA-DR and HLA-DQ, which present peptides to CD4+ T cells and account for the largest share of genetic susceptibility. But CD8+ cytotoxic T cells are the most abundant immune cell population infiltrating inflamed human islets, and it is HLA class I molecules — not class II — that present peptides to them. Among class I alleles, HLA-B39:06 is the single most strongly predisposing allele identified in T1D, associated with earlier disease onset and disproportionately common in Latino populations, where T1D incidence is rising. What makes this genetically strange is that B39:06 differs from two close relatives — the also-predisposing (but less so) B39:01, and the protective B38:01 — by only a handful of amino acids, despite the three sharing greater than 97% identity. Sharma’s talk was about what those few amino acids actually do, physically, inside the peptide-binding groove.
The basic architecture of any MHC class I molecule is an alpha-1 and alpha-2 helix pair forming a peptide-binding groove, subdivided into pockets labeled A through F. Sharma’s work concentrates on the F pocket — the pocket at the groove’s C-terminal end that anchors the last residue of a bound peptide — because this is exactly where B39:06 and B39:01 differ: B39:06 carries a bulky tryptophan at position 95, while B39:01 (and B38:01) carry a much smaller leucine at that position. To compare the two structurally, Sharma’s team first needed a peptide that both alleles would bind. They identified NRVMLPKA — derived from the human protein NLRP2 and eluted directly from C1R cells in the DiLorenzo lab — as the strongest known binder to B39:06 (IC50 = 14 nM) that also binds B*39:01 (IC50 = 35 nM), making it an ideal comparative tool.
Producing crystallizable protein required real troubleshooting: a single-chain, disulfide-trapped HLA-B*39:06 construct (via a Tyr84Cys mutation linking peptide to the MHC heavy chain) was expressed in FreeStyle 293 cells and purified by nickel-affinity and gel filtration chromatography, but early preparations resisted crystallization until the team recognized and removed a glycosylation site at position 86 using PNGase F. The deglycosylated protein yielded two distinct crystal forms (space groups C222₁ and P2₁2₁2₁), diffracted at a synchrotron beamline, and solved to 1.7 Å resolution using the CCP4i software suite and visualized in PyMOL.
The resulting structure clarified something the field had assumed differently for other MHC class I molecules: rather than the canonical position-9 anchor seen in most previously solved class I structures, NRVMLPKA is an 8-mer, and its C-terminal alanine at position 8 — not a position-9 residue — serves as the dominant anchor, forming strong hydrogen bonds with Asp80, Lys146, and Tyr147. Arginine at position 2 is the primary N-terminal anchor (hydrogen-bonding into the B pocket via Gln45, Asp63, and Ser24), with valine at position 3 as a secondary anchor. Methionine at position 4 and lysine at position 7 remain solvent-exposed — meaning these are the residues actually available for T cell receptor contact. Notably, this 8-mer preference lines up with the only known B39:06-restricted diabetogenic T cell epitope, MRLLA, itself an 8-mer — reinforcing that B39:06 has a genuine, biologically relevant preference for 8-mer peptides rather than the 9-mers typically favored by other class I alleles.
The comparative payoff came from the F pocket itself: B39:06’s bulky tryptophan-95 sterically restricts the pocket, meaning only small C-terminal residues (like alanine) fit — explaining why B39:06 favors 8-mer, alanine-anchored peptides. B39:01’s smaller leucine-95 opens up more room, favoring larger C-terminal residues (leucine, in a structural model built by superimposing NRVMLPKA onto a previously solved B39:01 structure). Because a full B38:01 crystal proved difficult to obtain, Sharma instead built a structural model: B38:01 also carries leucine at position 95, but its F pocket is comparatively neutral and larger, disfavoring basic residues while accommodating bulkier ones — meaning that despite sharing leucine-95 with B39:01, B38:01 preferentially binds a different peptide repertoire. Consistent with this, all three allotypes showed differential binding to peptides derived from beta cell autoantigens (including insulin and glucose-6-phosphatase 2, per the published paper), tying the structural differences directly to differences in which autoantigen peptides each allele can present to autoreactive CD8+ T cells.
🎯 Core Premise
X-ray crystal structures of HLA-B39:06 (1.7 Å resolution) bound to an 8-mer NLRP2-derived peptide, compared against HLA-B39:01 and a structural model of the protective HLA-B38:01, reveal that a single bulky tryptophan at F-pocket position 95 in B39:06 restricts the pocket to small C-terminal residues (favoring alanine-anchored 8-mers), while the smaller leucine-95 shared by B39:01 and B38:01 permits larger residues and a distinct peptide repertoire — with B38:01's additional groove differences further disfavoring basic residues. Because these three alleles — despite >97% sequence identity — differ in which peptides they can present, and because they show differential binding to beta cell autoantigen-derived peptides, the tiny structural differences between them translate directly into differences in which autoreactive CD8+ T cell responses each allele can support: the molecular basis for why B39:06 is the most aggressive class I T1D risk allele known, while B*38:01 is protective.
🌟 Why This Talk Matters to T1D Scientists and Clinicians
For scientists: Structural biology transformed understanding of class II–mediated T1D risk years ago, when crystal structures of HLA-DQ8 and HLA-DQ2 revealed how an unusual empty position 57 in DQ8’s groove creates its risk-conferring peptide-binding preferences. Sharma’s work opens the equivalent chapter for class I. With atomic-resolution structures of B39:06 and B39:01 now in hand — plus a structural model of protective B*38:01 — the field has a physical scaffold for mapping autoreactive CD8+ T cell responses, designing peptide-binding inhibitors, and explaining, mechanistically, why a two-decade-old genetic association has taken this long to become structurally legible. The F pocket finding is especially consequential: because C-terminal anchor residues are typically the single most important determinant of whether a peptide binds an MHC molecule stably enough to reach the cell surface, a small geometric difference here has outsized downstream consequences for the entire presented peptide repertoire — and for which autoreactive T cells get activated in the first place.
For clinicians: The translational logic, while early, is direct. If specific beta cell peptides bind B39:06 preferentially and drive the CD8+ T cell responses that destroy beta cells, those peptides become candidate biomarkers for tracking autoreactive T cell activity in B39:06-positive individuals — potentially before clinical onset. Structure-guided small molecules or peptide mimetics could, in principle, competitively block the F pocket and prevent autoantigen presentation without broadly immunosuppressing the patient — an approach Sharma’s group is actively pursuing via a compound-library screen. And because B*39:06 is disproportionately common in Latino populations, a group historically underrepresented in T1D research, this structural program has a direct path toward addressing a population-specific gap in risk stratification and, eventually, in immunosuppression-dosing decisions for interventions like islet transplantation.
3️⃣ Big Takeaways
Two or three amino acid differences are enough to convert the most aggressive known HLA class I T1D risk allele into a protective one — and the F pocket is where that difference lives. HLA-B39:06, B39:01, and B38:01 share more than 97% amino acid identity, yet range from strongly predisposing (B39:06) to protective (B38:01). The crystal structures show this comes down largely to residue 95 in the F pocket: a bulky tryptophan in B39:06 sterically restricts the pocket to small C-terminal residues, while a smaller leucine in the other two allotypes opens the pocket to larger residues — directly shaping which peptides each allele can stably present.
HLA-B39:06 has a genuine structural preference for 8-mer, alanine-anchored peptides — overturning the canonical assumption that position 9 is always the dominant anchor in class I peptide binding. Using an 8-mer peptide (NRVMLPKA) that binds both B39:06 and B39:01, the structure shows alanine at position 8 (not a position-9 residue) forms the strongest anchoring hydrogen bonds at the C-terminus, while methionine-4 and lysine-7 remain solvent-exposed for TCR contact. This matches the only known B39:06-restricted diabetogenic T cell epitope, MRLLA — itself an 8-mer — giving the structural finding direct biological grounding.
The structural differences between risk and protective alleles translate into differential presentation of actual beta cell autoantigen peptides — including insulin and glucose-6-phosphatase 2 — meaning the molecular story isn’t just about general immunogenicity but about specific capacity to display the peptides autoreactive T cells are trained to recognize. This sets up a concrete translational pipeline already underway in Sharma’s lab: a ~5,000-compound library screen targeting the F pocket for structure-guided blockers, a collaboration with Dr. Sally Kent (UMass Chan) to identify patient-derived B39:06-restricted T cell epitopes and eventually solve full TCR–peptide–MHC ternary complexes, and population-specific peptide-binding studies motivated by GWAS data at Einstein showing B39:06 is predominant in the Latino population.
❓ Key Questions from the Discussion
Could this structural work eventually become a clinical assay for stratifying autoimmune aggressiveness — for example, to guide immunosuppression dosing around future islet transplants? An audience member framed this in terms of minimizing immunosuppressant burden by predicting a given patient’s rate of autoimmunity ahead of a transplant. Sharma noted that Einstein has a large ongoing GWAS effort in T1D and has found that B*39:06 is predominant in the Latino population, which is highly predisposed; the lab has begun working out which peptides would be most useful for a population-specific assay, with the goal of building toward that kind of clinical tool as more data accumulates.
Is the peptide NRVMLPKA, or any of its mimics, a known T1D epitope? Ky Gerder (Medical College of Wisconsin) asked this directly. Sharma explained the peptide was eluted from both B39:06 and B39:01 as their strongest binder, with an IC50 comparable to known T cell epitopes, but that confirming true mimicry will require completing ongoing work with the actual diabetogenic epitope MRLLA — at which point a direct comparison will be possible.
If the goal is structure-guided therapeutics, is blocking the F pocket the best molecular handle, or are there other more selectively targetable sites in the groove? A questioner pushed on whether F-pocket blockade risks broader immune effects versus more selective alternatives. Sharma said her group is currently screening a library of roughly 5,000 compounds and does not yet know which will show the best inhibition, though she expects the F pocket to be the most promising target given that it is the site of the sharpest structural divergence between B*39:06 and the other allotypes; a definitive answer awaits further screening data.
Does the difference between predisposing and protective HLA-B alleles come down to different epitope preferences? Peter Lindqvist (Benaroya Research Institute) asked this. Sharma agreed this is the core logic: because the mature alleles differ in the amino acids lining their pockets, they cannot be expected to present the same peptide repertoire, and epitope preference will vary allele by allele.
Do you plan to test point mutations — for example, at the key tryptophan-95 residue — to see their effect on binding affinity? Ky Gerder also asked this. Sharma said this hadn’t been done yet but agreed it was an interesting next step, speculating that altering tryptophan-95 specifically could substantially change B*39:06’s binding behavior, since it’s the residue most responsible for the allele’s distinctive F pocket geometry.
Are you pursuing full TCR–peptide–MHC ternary complex structures, and what would that reveal about where the true risk-conferring features live? A questioner noted that understanding TCR recognition ultimately requires the ternary complex, not just the peptide-MHC structure. Sharma confirmed an active collaboration with Dr. Sally Kent at UMass Chan Medical School, who works on patient-derived B*39:06-restricted T cell epitopes; preliminary studies are just beginning, with fuller results expected as the crystallography (which she noted can take anywhere from a single attempt to six months of condition optimization) matures.
Has this been tested in non-diabetic individuals, to see whether B39:06 carries risk outside the autoimmune T1D context? Dan Heller asked this. Sharma confirmed HLA-B39:06 is present in the general non-T1D population but is not highly predisposing outside the T1D context — prompting a brief exchange about how identical-twin studies might illuminate this further, with Sharma noting such personalized studies tend to be more resource-intensive than standard population studies.
🔗 3 TSS Talks That Connect With This One
The Search for Diabetes-Specific T-cell Repertoires — Michel Edwar Mickael, PhD (TheSugarScience T1D Th1nk Tank, January 2026) Mickael’s talk covers how T1D-associated TCR sequences are identified from the broader repertoire — the receptor side of the exact molecular handshake Sharma’s structures illuminate from the MHC side. Watching this alongside today’s talk completes the picture: which TCRs recognize which peptide-MHC complexes, and why.
Bart Roep, PhD — The Quest to Cure T1D: Antigen-Specific Immunotherapy and the Reverse Vaccine (TheSugarScience Podcast, Episode 53) Roep’s “reverse vaccine” concept — using specific beta cell peptides to restore tolerance rather than broadly immunosuppress — is the therapeutic paradigm Sharma’s structural work feeds most directly. Designing a reverse vaccine for B*39:06-positive individuals requires knowing exactly which peptides that allele presents to autoreactive T cells — the atomic-level knowledge Sharma’s crystal structures are building.
WAVE T1D: Multicenter RCT Combination Therapy in New-Onset Type 1 Diabetes (TheSugarScience Clinical Trial Th1nk Tank, February 2026) This talk covers the current front line of combination immunotherapy in new-onset T1D — therapies that broadly target the adaptive immune system. It provides the clinical contrast for Sharma’s structural program: today’s treatments aren’t HLA-restricted, but the next generation of precision immunotherapy may need to specifically target B*39:06-restricted autoreactive responses, which is exactly the structural groundwork this talk describes.
🔔 Subscribe to The Sugar Science newsletter to get the latest T1D research drops straight to your inbox.